Variant report

Variant	rs6582658
Chromosome Location	chr12:46856095-46856096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46777826..46780308-chr12:46853985..46856424,2	MCF-7	breast:
2	chr12:46763417..46766868-chr12:46854687..46856582,3	K562	blood:
3	chr12:46850217..46852233-chr12:46852801..46856137,3	K562	blood:
4	chr12:46763417..46765337-chr12:46853370..46857226,3	K562	blood:
5	chr12:46854831..46858483-chr12:46859173..46862265,4	MCF-7	breast:
6	chr12:46764825..46767515-chr12:46854638..46860372,7	MCF-7	breast:
7	chr12:46848665..46851619-chr12:46853781..46857683,5	MCF-7	breast:
8	chr12:46766063..46767020-chr12:46856078..46856945,2	MCF-7	breast:
9	chr12:46854860..46856983-chr12:46864857..46866385,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10748448	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10748450	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10785627	0.88[EUR][1000 genomes]
rs10785628	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785629	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880967	0.87[EUR][1000 genomes]
rs10880968	0.87[EUR][1000 genomes]
rs10880969	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs10880970	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10880971	0.91[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880974	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11183478	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183479	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183483	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183484	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11183488	0.91[EUR][1000 genomes]
rs11183502	0.88[AMR][1000 genomes]
rs11183503	0.86[AMR][1000 genomes]
rs11183504	0.86[AMR][1000 genomes]
rs1125909	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11837427	0.88[AMR][1000 genomes]
rs12099669	0.84[EUR][1000 genomes]
rs12298616	0.90[EUR][1000 genomes]
rs12313929	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12314541	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12319162	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12822345	0.86[EUR][1000 genomes]
rs12824565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12827740	0.93[AMR][1000 genomes]
rs12832777	0.87[EUR][1000 genomes]
rs1472178	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1472179	0.85[EUR][1000 genomes]
rs1492895	0.87[EUR][1000 genomes]
rs2131371	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2220727	0.87[EUR][1000 genomes]
rs2408498	0.87[EUR][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3925101	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3936214	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4072304	0.87[EUR][1000 genomes]
rs4076247	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077708	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4427617	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs4768119	0.86[EUR][1000 genomes]
rs4768122	0.87[EUR][1000 genomes]
rs4768123	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768699	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4768709	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4768710	0.87[EUR][1000 genomes]
rs4768711	0.81[EUR][1000 genomes]
rs4768712	0.87[EUR][1000 genomes]
rs4768713	0.88[EUR][1000 genomes]
rs4768714	0.88[EUR][1000 genomes]
rs4768716	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4768717	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768718	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768719	0.91[EUR][1000 genomes]
rs4768723	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768725	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768726	0.88[AMR][1000 genomes]
rs4768727	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768728	0.88[AMR][1000 genomes]
rs4768729	0.88[AMR][1000 genomes]
rs4768730	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6582641	0.82[EUR][1000 genomes]
rs6582643	0.81[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6582646	0.87[EUR][1000 genomes]
rs6582657	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582659	0.83[AMR][1000 genomes]
rs6582660	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6582661	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6582663	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7134289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7311504	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7312259	0.85[EUR][1000 genomes]
rs7485580	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7485599	0.86[EUR][1000 genomes]
rs7486495	0.88[EUR][1000 genomes]
rs7486532	0.91[EUR][1000 genomes]
rs7486580	0.88[EUR][1000 genomes]
rs7486915	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7487877	0.86[EUR][1000 genomes]
rs7488144	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7488450	0.87[EUR][1000 genomes]
rs7488577	0.88[AMR][1000 genomes]
rs7489242	0.87[EUR][1000 genomes]
rs7954645	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7956314	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7959731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7960808	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7964767	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7968897	0.87[EUR][1000 genomes]
rs7980455	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs9669404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9706162	0.88[AMR][1000 genomes]
rs9706460	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9706520	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9971879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46866000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:46850000-46860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:46850600-46859200	Weak transcription	Stomach Mucosa	stomach
5	chr12:46852400-46856200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:46853200-46867400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:46853600-46856400	Weak transcription	NHLF	lung
8	chr12:46853600-46857600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr12:46853800-46857200	Enhancers	Fetal Heart	heart
10	chr12:46853800-46857200	Enhancers	Fetal Lung	lung
11	chr12:46853800-46858600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:46853800-46862600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:46854000-46857000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:46854000-46857000	Enhancers	Hela-S3	cervix
15	chr12:46854000-46858400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:46854200-46856200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr12:46854200-46856800	Weak transcription	Fetal Stomach	stomach
18	chr12:46854200-46860800	Weak transcription	HUVEC	blood vessel
19	chr12:46854400-46856800	Weak transcription	Thymus	Thymus
20	chr12:46854600-46856200	Enhancers	Psoas Muscle	Psoas
21	chr12:46854600-46856600	Enhancers	Primary T cells from cord blood	blood
22	chr12:46854600-46856600	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:46854600-46857000	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:46854600-46857000	Enhancers	NHDF-Ad	bronchial
25	chr12:46854600-46857200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:46854600-46857600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:46854600-46857600	Enhancers	NHEK	skin
28	chr12:46854800-46856800	Enhancers	Fetal Kidney	kidney
29	chr12:46854800-46856800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:46854800-46856800	Weak transcription	Right Atrium	heart
31	chr12:46854800-46859200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:46854800-46864000	Weak transcription	Spleen	Spleen
33	chr12:46854800-46866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:46855000-46856600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:46855000-46857400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:46855000-46859200	Weak transcription	Liver	Liver
37	chr12:46855000-46860200	Weak transcription	GM12878-XiMat	blood
38	chr12:46855000-46863800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:46855200-46856200	Enhancers	HSMM	muscle
40	chr12:46855200-46856200	Enhancers	HSMMtube	muscle
41	chr12:46855200-46857000	Enhancers	Stomach Smooth Muscle	stomach
42	chr12:46855200-46857200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:46855200-46857200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:46855200-46857800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:46855400-46856200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr12:46855400-46856400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:46855400-46856600	Enhancers	Placenta	Placenta
48	chr12:46855400-46858800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:46855400-46863600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:46855400-46863800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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