Variant report

Variant	rs3741630
Chromosome Location	chr12:49073358-49073359
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49072667..49077768-chr12:49107571..49112359,8	MCF-7	breast:
2	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:
3	chr12:49059501..49061624-chr12:49071853..49074328,2	K562	blood:
4	chr12:49052583..49059422-chr12:49071692..49076510,9	K562	blood:
5	chr12:49052650..49057544-chr12:49071692..49076123,6	K562	blood:
6	chr12:49072639..49079132-chr12:49108469..49112073,12	K562	blood:
7	chr12:49049997..49051694-chr12:49071950..49074374,2	K562	blood:

Variant related genes	Relation type
ENSG00000139620	Chromatin interaction
ENSG00000207313	Chromatin interaction
ENSG00000206612	Chromatin interaction
ENSG00000129315	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10747554	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783273	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10783274	0.87[ASN][1000 genomes]
rs10783275	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783277	0.88[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs10783278	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783281	0.86[EUR][1000 genomes]
rs10875849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs10875850	0.92[ASN][1000 genomes]
rs10875852	0.97[ASN][1000 genomes]
rs10875853	0.97[ASN][1000 genomes]
rs10875861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875862	0.93[ASN][1000 genomes]
rs1110432	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168657	0.90[ASN][1000 genomes]
rs11168665	0.97[ASN][1000 genomes]
rs11168674	0.95[ASN][1000 genomes]
rs11168697	0.85[ASN][1000 genomes]
rs11168698	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.89[ASN][1000 genomes]
rs12426435	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1316514	0.91[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1895995	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2114320	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2162317	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2277365	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2277366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2409085	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2898087	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3209584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35717253	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741629	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741632	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803025	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3943899	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4113946	0.92[ASN][1000 genomes]
rs4500528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4760735	0.92[ASN][1000 genomes]
rs4760737	0.93[ASN][1000 genomes]
rs4760739	0.91[ASN][1000 genomes]
rs4760740	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580690	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580692	0.81[EUR][1000 genomes]
rs6580693	0.89[EUR][1000 genomes]
rs7133756	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7136021	0.81[ASN][1000 genomes]
rs7138190	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7138930	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs7139236	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304711	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7305907	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7306604	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308699	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7314665	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954446	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7954548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7964546	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7966065	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7973824	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974151	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7974625	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975030	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.96[ASN][1000 genomes]
rs9634241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9634262	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv519053	chr12:49065727-49079470	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3741630	FAM186B	cis	cerebellum	SCAN
rs3741630	WNT10B	cis	Muscle Skeletal	GTEx
rs3741630	ADCY6	cis	parietal	SCAN
rs3741630	FLJ20436	cis	multi-tissue	Pritchard
rs3741630	ZNF641	cis	cerebellum	SCAN
rs3741630	SNORA2B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49041800-49073800	Strong transcription	Fetal Intestine Large	intestine
2	chr12:49045600-49073400	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr12:49058400-49074000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr12:49065800-49074600	Weak transcription	Aorta	Aorta
5	chr12:49066400-49075000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:49066600-49073400	Weak transcription	Gastric	stomach
7	chr12:49067600-49073400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:49068200-49073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:49069400-49074200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:49069800-49073800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr12:49070400-49073400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:49070400-49073400	Weak transcription	Fetal Intestine Small	intestine
13	chr12:49070400-49073600	Weak transcription	Spleen	Spleen
14	chr12:49070400-49075000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:49070600-49074600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
16	chr12:49070800-49074400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:49070800-49075000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:49071000-49073400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:49071000-49073400	Genic enhancers	NHDF-Ad	bronchial
20	chr12:49071000-49073800	Genic enhancers	Adipose Nuclei	Adipose
21	chr12:49071000-49074000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:49071000-49074000	Genic enhancers	Primary B cells from cord blood	blood
23	chr12:49071000-49074200	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:49071000-49074600	Genic enhancers	Colon Smooth Muscle	Colon
25	chr12:49071200-49074000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:49071200-49074000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:49071200-49074400	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr12:49071200-49074800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:49071400-49073400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:49071600-49073800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:49071600-49074200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
32	chr12:49071600-49074200	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr12:49071600-49074400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:49071600-49074400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:49071600-49074800	Genic enhancers	Osteobl	bone
36	chr12:49071800-49073400	Enhancers	Rectal Smooth Muscle	rectum
37	chr12:49071800-49073600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr12:49071800-49073800	Transcr. at gene 5' and 3'	HMEC	breast
39	chr12:49071800-49074000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:49071800-49074200	Genic enhancers	Rectal Mucosa Donor 31	rectum
41	chr12:49071800-49074400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:49071800-49074400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:49071800-49074400	Genic enhancers	Fetal Lung	lung
44	chr12:49071800-49074600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
45	chr12:49071800-49074800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:49072000-49074000	Genic enhancers	Liver	Liver
47	chr12:49072000-49074200	Genic enhancers	Brain Hippocampus Middle	brain
48	chr12:49072000-49074400	Transcr. at gene 5' and 3'	A549	lung
49	chr12:49072000-49074600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
50	chr12:49072000-49075000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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