Variant report

Variant	rs6477116
Chromosome Location	chr9:6842687-6842688
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6842488..6845236-chr9:6852172..6854079,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10117327	0.87[ASN][1000 genomes]
rs10119707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10120004	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10120603	0.92[ASN][1000 genomes]
rs10124035	0.92[ASN][1000 genomes]
rs10283675	0.88[JPT][hapmap]
rs10283920	0.90[JPT][hapmap]
rs10758805	0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10975819	0.90[JPT][hapmap]
rs10975835	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs10975852	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs10975854	0.93[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs10975855	0.98[ASN][1000 genomes]
rs11792093	0.90[ASN][1000 genomes]
rs11792706	0.94[JPT][hapmap]
rs11794756	0.95[JPT][hapmap]
rs12349015	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12352882	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs12353150	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs4143932	0.95[JPT][hapmap]
rs55680249	0.97[ASN][1000 genomes]
rs56261027	0.98[ASN][1000 genomes]
rs58872551	0.98[ASN][1000 genomes]
rs60449774	0.98[ASN][1000 genomes]
rs62533756	0.92[ASN][1000 genomes]
rs6477117	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6477118	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6477119	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[ASN][1000 genomes]
rs7031770	0.97[ASN][1000 genomes]
rs7031834	0.95[JPT][hapmap]
rs7048087	0.94[ASN][1000 genomes]
rs72701430	0.92[ASN][1000 genomes]
rs7846927	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7847729	0.95[JPT][hapmap]
rs7849234	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7852688	0.97[ASN][1000 genomes]
rs7872952	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	nsv892183	chr9:6811507-6855838	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv524069	chr9:6837912-6880263	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6795000-6863800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr9:6795400-6849600	Weak transcription	HMEC	breast
3	chr9:6814600-6845400	Weak transcription	Fetal Brain Male	brain
4	chr9:6815400-6852000	Weak transcription	NHDF-Ad	bronchial
5	chr9:6816000-6856000	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:6818800-6856000	Weak transcription	Psoas Muscle	Psoas
7	chr9:6819800-6853400	Weak transcription	Small Intestine	intestine
8	chr9:6820400-6845200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:6824200-6849200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:6824200-6849600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:6824200-6860000	Weak transcription	Hela-S3	cervix
12	chr9:6824400-6892000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:6825400-6849800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:6828000-6846000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:6831800-6849200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:6832000-6847400	Weak transcription	HSMMtube	muscle
17	chr9:6832000-6852800	Weak transcription	K562	blood
18	chr9:6834000-6854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:6835200-6845600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:6835200-6851200	Weak transcription	Placenta	Placenta
21	chr9:6835200-6851400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:6835200-6851800	Weak transcription	NHLF	lung
23	chr9:6835200-6854600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:6835200-6863800	Weak transcription	Brain Anterior Caudate	brain
25	chr9:6835400-6842800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:6835400-6845000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:6835400-6845800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:6835400-6849400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:6835400-6849600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:6835400-6849600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:6835400-6851600	Weak transcription	Fetal Brain Female	brain
32	chr9:6835400-6852200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:6835400-6855000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:6835400-6856400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:6835400-6863400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:6835400-6863400	Weak transcription	Ovary	ovary
37	chr9:6835400-6869200	Weak transcription	Right Ventricle	heart
38	chr9:6835400-6893200	Weak transcription	Colonic Mucosa	Colon
39	chr9:6835600-6842800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:6835600-6843200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:6835600-6845200	Weak transcription	Liver	Liver
42	chr9:6835600-6845200	Weak transcription	Gastric	stomach
43	chr9:6835600-6845200	Weak transcription	Pancreas	Pancrea
44	chr9:6835600-6845600	Weak transcription	Left Ventricle	heart
45	chr9:6835600-6845800	Weak transcription	Aorta	Aorta
46	chr9:6835600-6849000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:6835600-6849200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:6835600-6849400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr9:6835600-6849400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:6835600-6849400	Weak transcription	Dnd41	blood

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