Variant report

Variant	rs7955541
Chromosome Location	chr12:49796721-49796722
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49795862..49798729-chr12:49818439..49819958,2	MCF-7	breast:
2	chr12:49791986..49794949-chr12:49795587..49799517,5	MCF-7	breast:
3	chr12:49758199..49761031-chr12:49795852..49797859,2	K562	blood:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10160947	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10161131	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10506285	1.00[JPT][hapmap]
rs10783314	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs10875948	1.00[CHB][hapmap]
rs10875958	0.83[EUR][1000 genomes]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11168988	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169005	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11169008	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169009	0.85[EUR][1000 genomes]
rs11169014	0.84[EUR][1000 genomes]
rs11169015	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169017	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169027	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169043	0.85[EUR][1000 genomes]
rs11169045	0.84[EUR][1000 genomes]
rs11169048	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11169049	0.90[EUR][1000 genomes]
rs11169058	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs11169059	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs11169063	0.83[ASW][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs11611743	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615710	0.82[EUR][1000 genomes]
rs11830144	1.00[CHD][hapmap]
rs11834161	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11835037	1.00[CHB][hapmap]
rs11837234	1.00[CHB][hapmap]
rs12296440	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs12299282	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302036	0.83[ASN][1000 genomes]
rs12305716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12306118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306212	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306645	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12310129	1.00[JPT][hapmap]
rs12315996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12320284	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322319	1.00[ASN][1000 genomes]
rs12322335	1.00[CHB][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12581343	1.00[CHB][hapmap]
rs12581428	1.00[CHB][hapmap]
rs17123696	1.00[JPT][hapmap]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123764	1.00[CHD][hapmap]
rs17123790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874910	1.00[JPT][hapmap]
rs2236746	1.00[CHB][hapmap]
rs2270741	1.00[JPT][hapmap]
rs2272478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28450055	1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs4144469	1.00[JPT][hapmap]
rs57108124	1.00[ASN][1000 genomes]
rs57601151	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58095611	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59250459	1.00[ASN][1000 genomes]
rs60808917	0.82[EUR][1000 genomes]
rs61340540	1.00[ASN][1000 genomes]
rs6580707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580710	1.00[ASN][1000 genomes]
rs6580711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580715	0.84[EUR][1000 genomes]
rs6580716	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7132684	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133398	0.85[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap]
rs7139061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7294973	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7295162	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7295247	1.00[CHB][hapmap]
rs7295556	0.93[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73295291	1.00[ASN][1000 genomes]
rs73295300	1.00[ASN][1000 genomes]
rs73297209	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297210	1.00[ASN][1000 genomes]
rs73297243	1.00[ASN][1000 genomes]
rs7342318	1.00[CHB][hapmap]
rs7342365	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7342384	1.00[CHB][hapmap]
rs74089066	1.00[ASN][1000 genomes]
rs7488923	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7961032	0.83[ASN][1000 genomes]
rs7962951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965658	0.87[GIH][hapmap]
rs7969010	0.92[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970059	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7974420	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7975712	0.83[ASW][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7976165	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7980731	0.83[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49764000-49797600	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:49764000-49807400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:49764200-49804200	Weak transcription	Primary B cells from cord blood	blood
4	chr12:49764200-49840200	Weak transcription	Fetal Lung	lung
5	chr12:49764400-49822200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:49766600-49822200	Weak transcription	NH-A	brain
7	chr12:49768400-49819200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:49776000-49797000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:49781600-49810000	Weak transcription	Right Ventricle	heart
10	chr12:49783200-49804200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:49783400-49798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:49783600-49816400	Weak transcription	Left Ventricle	heart
13	chr12:49783800-49796800	Weak transcription	NHEK	skin
14	chr12:49784000-49804200	Weak transcription	GM12878-XiMat	blood
15	chr12:49784000-49806800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:49788000-49796800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:49788000-49822600	Weak transcription	HUVEC	blood vessel
18	chr12:49789200-49797600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:49790600-49797600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:49791000-49797600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:49791200-49797600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:49791400-49800800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:49791400-49819200	Weak transcription	Osteobl	bone
24	chr12:49791600-49796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:49791800-49817000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:49792200-49798600	Enhancers	A549	lung
27	chr12:49792800-49812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:49792800-49819200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:49792800-49822000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:49793000-49818600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:49793800-49798000	Enhancers	HepG2	liver
32	chr12:49794400-49797600	Weak transcription	Psoas Muscle	Psoas
33	chr12:49794400-49812400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:49795000-49806800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:49795800-49797000	Enhancers	Gastric	stomach
36	chr12:49796000-49797600	Enhancers	Hela-S3	cervix
37	chr12:49796000-49808200	Weak transcription	Lung	lung
38	chr12:49796200-49798400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:49796600-49797600	Weak transcription	K562	blood

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