Variant report

Variant	rs2799499
Chromosome Location	chr10:38246545-38246546
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	POLR2A	chr10:38246529-38246551	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:38146605..38148407-chr10:38246117..38248023,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266684	TF binding region
ENSG00000198105	Chromatin interaction
ENSG00000236514	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1007133	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10827831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs10827844	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11011354	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11011355	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11011366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11011384	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11011401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11011405	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11011426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11011431	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1148287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11492508	1.00[CEU][hapmap]
rs11523837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs11594000	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11597286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11598044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1208587	0.90[JPT][hapmap]
rs1208633	0.86[ASN][1000 genomes]
rs1208645	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs1208683	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1212108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12357256	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12359608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs12571785	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12763409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12768276	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12768391	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12782327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1322319	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1735621	0.93[ASN][1000 genomes]
rs1735629	0.97[ASN][1000 genomes]
rs1735641	0.97[ASN][1000 genomes]
rs1779075	0.91[ASN][1000 genomes]
rs2092993	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2092995	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2103936	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2142346	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2144845	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245081	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295872	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2474549	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505233	0.90[JPT][hapmap]
rs2505255	0.85[ASN][1000 genomes]
rs2738186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2738187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2738190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2738191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2738193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2738207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2738208	0.90[JPT][hapmap]
rs2738209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2738210	0.83[ASN][1000 genomes]
rs2738219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2738222	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749559	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2749569	0.86[ASN][1000 genomes]
rs2749575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749588	0.81[JPT][hapmap]
rs2749589	0.90[JPT][hapmap]
rs2749593	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2753878	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2753879	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2753880	0.97[ASN][1000 genomes]
rs2753882	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799495	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799501	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2799502	0.80[AMR][1000 genomes]
rs2799505	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799506	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799507	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799509	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2891586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3824585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs594594	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs596118	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615718	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615974	0.81[ASN][1000 genomes]
rs61857002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61858886	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs624359	0.90[JPT][hapmap]
rs628330	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633029	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs637255	0.90[JPT][hapmap]
rs647617	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs650873	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs656126	0.90[ASN][1000 genomes]
rs662928	0.81[JPT][hapmap]
rs675628	0.97[ASN][1000 genomes]
rs688608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7077222	0.85[AMR][1000 genomes]
rs7077233	0.85[AMR][1000 genomes]
rs72639538	0.85[AMR][1000 genomes]
rs9417267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9417268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9417283	0.83[ASN][1000 genomes]
rs9418297	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9418298	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9418299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised 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	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2799499	ZNF37A	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38236800-38249000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:38237800-38247200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr10:38238000-38248600	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:38238400-38253000	Weak transcription	Fetal Intestine Small	intestine
5	chr10:38238800-38248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:38239000-38247000	Strong transcription	Left Ventricle	heart
7	chr10:38239000-38249400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr10:38239200-38246600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr10:38239200-38248000	Strong transcription	Adipose Nuclei	Adipose
10	chr10:38239400-38247400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:38239400-38247800	Strong transcription	Brain Hippocampus Middle	brain
12	chr10:38239400-38248200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr10:38239600-38264400	Weak transcription	Fetal Heart	heart
14	chr10:38239600-38264600	Weak transcription	Stomach Mucosa	stomach
15	chr10:38240000-38246600	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr10:38240000-38247600	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:38240200-38247800	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:38240400-38246800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr10:38240400-38247600	Strong transcription	Fetal Lung	lung
20	chr10:38240400-38249200	Strong transcription	Ovary	ovary
21	chr10:38240600-38247400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr10:38240600-38247400	Strong transcription	NHDF-Ad	bronchial
23	chr10:38240600-38247800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr10:38240600-38248200	Strong transcription	Fetal Muscle Leg	muscle
25	chr10:38240800-38264000	Weak transcription	NHLF	lung
26	chr10:38241000-38246600	Strong transcription	Colon Smooth Muscle	Colon
27	chr10:38241000-38247400	Strong transcription	Brain Angular Gyrus	brain
28	chr10:38241000-38247400	Strong transcription	Brain Cingulate Gyrus	brain
29	chr10:38241000-38247800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr10:38241000-38248200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr10:38241200-38247400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr10:38241200-38247400	Strong transcription	Brain Anterior Caudate	brain
33	chr10:38241200-38249600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr10:38241800-38249000	Weak transcription	Small Intestine	intestine
35	chr10:38241800-38264400	Weak transcription	NHEK	skin
36	chr10:38242000-38248400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr10:38242200-38246600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:38242200-38253600	Weak transcription	Esophagus	oesophagus
39	chr10:38242200-38253800	Weak transcription	Pancreas	Pancrea
40	chr10:38242400-38247200	Strong transcription	Fetal Kidney	kidney
41	chr10:38242400-38247800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:38242400-38248200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:38242400-38248800	Strong transcription	Fetal Brain Female	brain
44	chr10:38242400-38253400	Weak transcription	Spleen	Spleen
45	chr10:38242400-38253600	Weak transcription	Gastric	stomach
46	chr10:38242600-38247400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr10:38242600-38248600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr10:38242600-38264400	Weak transcription	HUVEC	blood vessel
49	chr10:38242800-38246600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:38243000-38247400	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links