Variant report

Variant	rs6580716
Chromosome Location	chr12:49834150-49834151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49759541..49761666-chr12:49832483..49834672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 93 )
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];0.91[AMR][1000 genomes];0.98[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	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12315996	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12316170	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12318633	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12320284	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs12322319	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[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	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs4144469	1.00[JPT][hapmap]
rs57108124	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57601151	1.00[ASN][1000 genomes]
rs59250459	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340540	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580711	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];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7295162	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]
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];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73295291	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295300	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297209	1.00[ASN][1000 genomes]
rs73297210	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297243	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73301240	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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	0.86[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:47 , 50 per page) page: 1

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	chr12:49812600-49849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:49816000-49848800	Weak transcription	Fetal Kidney	kidney
6	chr12:49820400-49854400	Weak transcription	Dnd41	blood
7	chr12:49822800-49842600	Weak transcription	NHLF	lung
8	chr12:49823000-49835600	Weak transcription	HUVEC	blood vessel
9	chr12:49823000-49836200	Weak transcription	HMEC	breast
10	chr12:49823000-49840200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:49823000-49840200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:49823000-49854200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:49823000-49856000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
15	chr12:49823200-49856000	Weak transcription	NHEK	skin
16	chr12:49823200-49856400	Weak transcription	HSMM	muscle
17	chr12:49823400-49840000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:49823400-49854400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:49823400-49856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:49823400-49857400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:49823400-49876000	Weak transcription	Osteobl	bone
22	chr12:49825800-49839400	Weak transcription	Fetal Stomach	stomach
23	chr12:49828000-49863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:49829400-49855000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:49831200-49849000	Weak transcription	NH-A	brain
26	chr12:49831600-49852000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:49831800-49838400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:49832400-49834200	Enhancers	HepG2	liver
29	chr12:49832400-49839800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:49832600-49834200	Enhancers	Fetal Intestine Small	intestine
31	chr12:49832800-49835200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:49833000-49834200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:49833000-49849200	Weak transcription	Fetal Intestine Large	intestine
34	chr12:49833000-49849800	Weak transcription	K562	blood
35	chr12:49833200-49834200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr12:49833200-49834200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr12:49833200-49835400	Weak transcription	GM12878-XiMat	blood
38	chr12:49833400-49834200	Enhancers	Stomach Mucosa	stomach
39	chr12:49833400-49839200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:49833400-49848600	Weak transcription	Psoas Muscle	Psoas
41	chr12:49833600-49835400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:49833600-49835600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:49833600-49849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:49833600-49854600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:49833800-49834200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:49834000-49840000	Weak transcription	A549	lung
47	chr12:49834000-49849400	Weak transcription	Left Ventricle	heart

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