Variant report

Variant	rs6477109
Chromosome Location	chr9:6794938-6794939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10117618	0.80[CHB][hapmap];0.90[CHD][hapmap]
rs10120785	0.85[CHB][hapmap]
rs10283424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815467	0.80[CHB][hapmap]
rs10815468	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10975833	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975834	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11792238	0.88[ASN][1000 genomes]
rs11792731	0.92[ASN][1000 genomes]
rs11795163	0.92[ASN][1000 genomes]
rs12001316	0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12115812	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12351262	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13290274	0.81[AMR][1000 genomes]
rs2918178	0.87[AMR][1000 genomes]
rs4740855	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4740858	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4740859	0.99[ASN][1000 genomes]
rs4742259	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs4742260	0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs4742263	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742264	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56836206	0.81[AMR][1000 genomes]
rs58001441	0.87[ASN][1000 genomes]
rs62567973	0.89[ASN][1000 genomes]
rs6477107	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs7037259	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7045189	0.81[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs7045291	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7851230	0.99[ASN][1000 genomes]
rs7851383	0.99[ASN][1000 genomes]
rs7851954	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858345	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv1028402	chr9:6542253-6874231	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1018308	chr9:6544766-6869653	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1015462	chr9:6544766-6874231	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
6	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
7	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
8	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
9	nsv1029929	chr9:6573752-6852349	Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
10	nsv539969	chr9:6573752-6852349	Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
11	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
12	esv2758626	chr9:6576991-6838660	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
13	esv2759661	chr9:6576991-6845561	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
14	nsv1031417	chr9:6584138-6823129	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
15	nsv539970	chr9:6584138-6823129	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
16	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
17	nsv1021933	chr9:6605417-6824468	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
18	nsv1018845	chr9:6609578-6829592	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
19	nsv1033323	chr9:6630626-6824468	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
20	esv2752309	chr9:6670448-6908200	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
21	nsv982630	chr9:6672217-6796787	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
22	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
23	nsv870332	chr9:6694842-6911550	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
24	nsv1016109	chr9:6712314-6924843	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
25	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
26	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
27	nsv1018557	chr9:6723728-6891136	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
28	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
29	nsv892182	chr9:6739489-6811507	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
30	esv2757308	chr9:6743440-6845561	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
31	nsv1032676	chr9:6745551-6864365	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
32	nsv466115	chr9:6750556-6859189	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
33	nsv613256	chr9:6750556-6859189	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
34	nsv824840	chr9:6762285-6805457	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
35	esv35116	chr9:6769429-6798091	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
36	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
37	nsv1033692	chr9:6784144-6863403	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv1027705	chr9:6784659-6863403	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
39	nsv824841	chr9:6793104-6795060	Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6774200-6806200	Weak transcription	Aorta	Aorta
2	chr9:6783800-6799000	Weak transcription	Spleen	Spleen
3	chr9:6787400-6810000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:6788200-6810600	Weak transcription	Small Intestine	intestine
5	chr9:6788200-6819400	Weak transcription	K562	blood
6	chr9:6789000-6796400	Weak transcription	Brain Angular Gyrus	brain
7	chr9:6789000-6796400	Weak transcription	Psoas Muscle	Psoas
8	chr9:6789000-6797400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:6789000-6797600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:6789000-6799000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:6789000-6799200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:6789000-6799200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:6789000-6805400	Weak transcription	Brain Anterior Caudate	brain
14	chr9:6789000-6805600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:6789000-6805800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:6789000-6805800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:6789000-6806600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:6789000-6806600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:6789000-6808600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:6789000-6831800	Weak transcription	Osteobl	bone
21	chr9:6789200-6797000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:6789200-6799200	Weak transcription	NHLF	lung
23	chr9:6789200-6799400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:6789200-6802200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:6789200-6823400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:6789200-6834200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:6789200-6834400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:6791400-6818400	Weak transcription	Pancreas	Pancrea
29	chr9:6791600-6809800	Weak transcription	Stomach Mucosa	stomach
30	chr9:6792000-6831400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:6792600-6795200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:6792600-6795200	Strong transcription	Fetal Thymus	thymus
33	chr9:6792600-6796800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr9:6792600-6797000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:6792600-6797400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:6792600-6797800	Strong transcription	Primary B cells from cord blood	blood
37	chr9:6792800-6795200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr9:6792800-6795200	Strong transcription	Fetal Muscle Leg	muscle
39	chr9:6792800-6795400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:6792800-6795600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr9:6792800-6796000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:6792800-6796200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr9:6792800-6796600	Strong transcription	Primary T cells from cord blood	blood
44	chr9:6792800-6796800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr9:6792800-6797200	Strong transcription	Thymus	Thymus
46	chr9:6792800-6798400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:6793000-6795000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr9:6793000-6795200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr9:6793000-6795400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr9:6793000-6795400	Strong transcription	HMEC	breast

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