Variant report

Variant	rs7628476
Chromosome Location	chr3:398423-398424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:398420-398570	RPTEC	kidney:	n/a	n/a

Variant related genes	Relation type
CHL1	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11129587	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12490993	0.80[EUR][1000 genomes]
rs13061580	0.87[JPT][hapmap]
rs13066759	0.87[JPT][hapmap]
rs13078884	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs13083718	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1353810	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1874947	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060312	0.92[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2117044	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34177368	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35073337	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3773385	0.84[CEU][hapmap]
rs3773386	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3773388	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773390	0.83[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3773391	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773392	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3773393	0.85[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3773395	0.85[JPT][hapmap]
rs4105570	0.82[JPT][hapmap]
rs4685627	0.96[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442794	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs892296	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823348	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9824311	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9824442	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9826896	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839027	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9841789	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010433	chr3:60333-480173	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv469898	chr3:63411-928456	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv2757853	chr3:71156-798503	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2759122	chr3:71156-798503	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949001	chr3:73603-780291	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv589242	chr3:89412-430682	Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv536270	chr3:93948-594328	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv536271	chr3:93948-838994	Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv498052	chr3:93949-910076	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1005694	chr3:101277-431496	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1009662	chr3:101277-477045	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1012326	chr3:101277-560678	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1012165	chr3:101277-674386	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv536285	chr3:113832-538808	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv536286	chr3:113832-793686	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv536287	chr3:127519-726705	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
17	nsv532555	chr3:212711-1060145	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
18	nsv482709	chr3:216030-421075	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv876287	chr3:226067-1081998	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv533425	chr3:232270-650502	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
21	nsv491804	chr3:232496-1197682	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
22	nsv997392	chr3:236668-438354	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1004703	chr3:236668-969518	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
24	nsv834589	chr3:277188-437186	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv1004600	chr3:285783-649454	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
26	nsv532556	chr3:286300-1250834	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
27	nsv531611	chr3:287500-1138964	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
28	nsv1005290	chr3:288775-991003	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
29	nsv1010033	chr3:300020-611720	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
30	nsv536291	chr3:300020-611720	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
31	nsv589291	chr3:320201-1128796	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
32	nsv1003414	chr3:329018-544279	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
33	nsv536293	chr3:329018-544279	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
34	nsv1010802	chr3:329018-611720	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
35	nsv536294	chr3:329018-611720	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
36	nsv1014934	chr3:329069-594328	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
37	nsv536295	chr3:329069-594328	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
38	nsv1003266	chr3:369953-969518	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
39	nsv536296	chr3:369953-969518	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
40	nsv589293	chr3:397731-475007	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:366000-410400	Weak transcription	Brain Anterior Caudate	brain
2	chr3:385200-420200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:389200-404000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:392400-409000	Weak transcription	Fetal Brain Female	brain
5	chr3:392800-406400	Weak transcription	Brain Germinal Matrix	brain
6	chr3:393000-403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:396000-399000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:396600-400800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:396600-401400	Weak transcription	Fetal Brain Male	brain
10	chr3:396800-400000	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:397200-415000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:397400-398600	Weak transcription	NH-A	brain
13	chr3:397600-403400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:397600-453400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:397800-399000	Enhancers	Ovary	ovary
16	chr3:398000-398600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:398000-399000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:398000-399200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:398000-400400	Enhancers	Colon Smooth Muscle	Colon
20	chr3:398200-399200	Enhancers	Stomach Smooth Muscle	stomach
21	chr3:398200-400000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:398400-398600	Enhancers	Brain Hippocampus Middle	brain
23	chr3:398400-398600	Enhancers	HSMM	muscle
24	chr3:398400-399000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:398400-399000	Enhancers	Fetal Muscle Leg	muscle
26	chr3:398400-415000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links