Variant report

Variant	rs10009502
Chromosome Location	chr4:94750058-94750059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10006848	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10010361	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs10010675	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs10015253	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10019131	0.88[AFR][1000 genomes]
rs10021588	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10024195	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10024650	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10032384	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap]
rs12499415	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs12499509	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap]
rs1439554	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550353	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550354	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17297269	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28703171	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3923305	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs4693345	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532435	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6810762	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6828743	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836045	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850864	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7688938	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9284594	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9307129	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9307130	0.85[EUR][1000 genomes]
rs9307131	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9307132	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs992917	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs992918	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9991074	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap]
rs9991641	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9992307	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008055	chr4:94169131-95030074	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931979	chr4:94289958-95121723	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv821636	chr4:94439636-95116590	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv1792557	chr4:94738158-95027272	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:94748400-94750400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:94748400-94750600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr4:94748400-94751000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:94748400-94751000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:94748400-94751000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr4:94748400-94751000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
7	chr4:94748400-94751200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:94748400-94751600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr4:94748400-94751800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:94748600-94750400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:94748600-94750400	Bivalent/Poised TSS	Psoas Muscle	Psoas
12	chr4:94748600-94750800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:94748600-94751000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr4:94748800-94750200	Flanking Bivalent TSS/Enh	NHEK	skin
15	chr4:94748800-94750400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:94748800-94750400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:94749000-94750200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr4:94749000-94751800	Bivalent Enhancer	Fetal Lung	lung
19	chr4:94749200-94750400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr4:94749200-94750400	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr4:94749200-94750400	Bivalent/Poised TSS	A549	lung
22	chr4:94749200-94750800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:94749200-94751000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:94749200-94751000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:94749200-94751000	Bivalent Enhancer	Liver	Liver
26	chr4:94749200-94751200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
27	chr4:94749200-94751400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
28	chr4:94749200-94751400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
29	chr4:94749200-94751600	Bivalent Enhancer	Fetal Brain Male	brain
30	chr4:94749400-94750200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:94749400-94750200	Active TSS	Aorta	Aorta
32	chr4:94749400-94750200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
33	chr4:94749400-94750200	Bivalent/Poised TSS	HepG2	liver
34	chr4:94749400-94750200	Bivalent/Poised TSS	HSMM	muscle
35	chr4:94749400-94750400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:94749400-94750400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:94749400-94750400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:94749400-94750400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
39	chr4:94749400-94750400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
40	chr4:94749400-94750400	Flanking Bivalent TSS/Enh	Left Ventricle	heart
41	chr4:94749400-94750600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr4:94749400-94750600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:94749400-94750600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr4:94749400-94750800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
45	chr4:94749400-94750800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:94749400-94750800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr4:94749400-94750800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr4:94749400-94750800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
49	chr4:94749400-94750800	Bivalent Enhancer	Small Intestine	intestine
50	chr4:94749400-94751000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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