Variant report

Variant	rs7295162
Chromosome Location	chr12:49823119-49823120
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49760202..49762803-chr12:49821694..49823885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10160947	0.83[ASN][1000 genomes]
rs10161131	0.83[ASN][1000 genomes]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10506285	1.00[JPT][hapmap]
rs10875948	1.00[CHB][hapmap]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap]
rs11168988	1.00[ASN][1000 genomes]
rs11169015	1.00[ASN][1000 genomes]
rs11169016	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169017	1.00[ASN][1000 genomes]
rs11169027	1.00[ASN][1000 genomes]
rs11169048	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11169058	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11169059	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11611743	1.00[ASN][1000 genomes]
rs11830144	1.00[CHD][hapmap]
rs11834161	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835037	1.00[CHB][hapmap]
rs11837234	1.00[CHB][hapmap]
rs12296440	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12299282	1.00[ASN][1000 genomes]
rs12301632	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12302036	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12305716	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs12306118	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306212	1.00[ASN][1000 genomes]
rs12306645	1.00[ASN][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12310129	1.00[JPT][hapmap]
rs12310836	0.84[AMR][1000 genomes]
rs12314428	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12315996	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12316170	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12318633	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12320284	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs12322319	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322335	1.00[CHB][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][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	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs28450055	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs4144469	1.00[JPT][hapmap]
rs57108124	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57601151	1.00[ASN][1000 genomes]
rs59250459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340540	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580709	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580710	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580711	1.00[ASN][1000 genomes]
rs6580716	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132684	1.00[ASN][1000 genomes]
rs7139061	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7294648	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7294973	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];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7295247	1.00[CHB][hapmap]
rs7309997	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73295291	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295300	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297209	1.00[ASN][1000 genomes]
rs73297210	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73301240	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7342318	1.00[CHB][hapmap]
rs7342365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342384	1.00[CHB][hapmap]
rs74089066	1.00[ASN][1000 genomes]
rs7955541	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7961032	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7962951	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7964718	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7969010	0.91[CEU][hapmap];1.00[ASN][1000 genomes]
rs7969099	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7976165	0.93[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];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS 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	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49764200-49840200	Weak transcription	Fetal Lung	lung
2	chr12:49798400-49856000	Weak transcription	Primary T cells from cord blood	blood
3	chr12:49798600-49840000	Weak transcription	Hela-S3	cervix
4	chr12:49810800-49831400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:49812600-49829200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:49812600-49849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:49816000-49848800	Weak transcription	Fetal Kidney	kidney
8	chr12:49816200-49833000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:49816600-49826400	Weak transcription	Small Intestine	intestine
10	chr12:49817400-49827800	Weak transcription	Fetal Brain Female	brain
11	chr12:49817600-49832400	Weak transcription	HepG2	liver
12	chr12:49819600-49828600	Weak transcription	Fetal Intestine Small	intestine
13	chr12:49820000-49825200	Weak transcription	Fetal Stomach	stomach
14	chr12:49820000-49828400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:49820200-49828600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:49820400-49825600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:49820400-49826400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:49820400-49854400	Weak transcription	Dnd41	blood
19	chr12:49822000-49823400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:49822200-49823200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:49822200-49823200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr12:49822200-49823400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:49822200-49823400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:49822200-49823600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:49822400-49823200	Enhancers	NHEK	skin
26	chr12:49822400-49823400	Enhancers	HSMMtube	muscle
27	chr12:49822600-49823400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:49822600-49823400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:49822600-49823400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:49822600-49823400	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:49822600-49823400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:49822600-49823400	Enhancers	Fetal Muscle Leg	muscle
33	chr12:49822600-49823400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr12:49822600-49823400	Enhancers	Osteobl	bone
35	chr12:49822800-49823200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:49822800-49823200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:49822800-49823200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:49822800-49823200	Enhancers	HSMM	muscle
39	chr12:49822800-49823400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:49822800-49823400	Enhancers	Brain Cingulate Gyrus	brain
41	chr12:49822800-49842600	Weak transcription	NHLF	lung
42	chr12:49823000-49823200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:49823000-49823200	Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:49823000-49823400	Active TSS	GM12878-XiMat	blood
45	chr12:49823000-49825600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:49823000-49832400	Weak transcription	A549	lung
47	chr12:49823000-49835600	Weak transcription	HUVEC	blood vessel
48	chr12:49823000-49836200	Weak transcription	HMEC	breast
49	chr12:49823000-49840200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:49823000-49840200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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