Variant report

Variant	rs3087577
Chromosome Location	chr12:67709965-67709966
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:67708479..67710797-chr12:67718354..67720777,2	MCF-7	breast:
2	chr12:67709812..67710332-chr4:99531489..99532009,2	MCF-7	breast:
3	chr12:67661690..67663696-chr12:67708706..67710365,2	K562	blood:
4	chr12:67708442..67711026-chr12:67711731..67713764,2	MCF-7	breast:
5	chr12:67708053..67712275-chr12:67717926..67720355,3	K562	blood:

Variant related genes	Relation type
ENSG00000111530	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10878598	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11176668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11176669	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176670	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176672	0.87[AFR][1000 genomes]
rs11176673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11176686	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11176689	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176693	0.81[AFR][1000 genomes]
rs11176703	1.00[ASN][1000 genomes]
rs11176704	1.00[ASN][1000 genomes]
rs11176705	1.00[ASN][1000 genomes]
rs11176707	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11176711	0.95[ASN][1000 genomes]
rs12299097	0.87[AFR][1000 genomes]
rs12302564	1.00[ASN][1000 genomes]
rs12305377	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306657	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311150	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12313282	0.89[AFR][1000 genomes]
rs12314146	1.00[ASN][1000 genomes]
rs12321396	0.89[AFR][1000 genomes]
rs3736630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55646172	0.95[ASN][1000 genomes]
rs55809526	0.95[ASN][1000 genomes]
rs55809587	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55906716	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55978724	0.95[ASN][1000 genomes]
rs56224819	0.95[ASN][1000 genomes]
rs56728872	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58114937	0.95[ASN][1000 genomes]
rs60009568	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60072946	0.95[ASN][1000 genomes]
rs60077199	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60104343	0.91[ASN][1000 genomes]
rs60971316	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61195985	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61219299	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61281993	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137520	0.98[ASN][1000 genomes]
rs7296364	0.95[ASN][1000 genomes]
rs7298244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7307353	0.95[ASN][1000 genomes]
rs7312708	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7954050	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976686	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7978989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv756	chr12:67703587-67744743	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67681000-67714200	Weak transcription	Spleen	Spleen
2	chr12:67682200-67715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:67682600-67710600	Weak transcription	Right Ventricle	heart
4	chr12:67683400-67710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:67686000-67717000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:67686200-67711200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:67686200-67716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:67686400-67716000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:67687800-67715400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:67688200-67711400	Strong transcription	Placenta	Placenta
11	chr12:67688200-67717000	Strong transcription	NH-A	brain
12	chr12:67688400-67716000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:67688800-67711800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:67691000-67716000	Weak transcription	Fetal Intestine Small	intestine
15	chr12:67698600-67714000	Strong transcription	Fetal Thymus	thymus
16	chr12:67700000-67713200	Weak transcription	Pancreas	Pancrea
17	chr12:67700000-67715400	Weak transcription	Lung	lung
18	chr12:67700000-67716200	Weak transcription	Fetal Stomach	stomach
19	chr12:67700200-67710800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:67700200-67717600	Weak transcription	Gastric	stomach
21	chr12:67700400-67712800	Weak transcription	Ovary	ovary
22	chr12:67700600-67712400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:67700600-67712400	Weak transcription	Esophagus	oesophagus
24	chr12:67700600-67716000	Weak transcription	Aorta	Aorta
25	chr12:67700600-67717400	Weak transcription	Psoas Muscle	Psoas
26	chr12:67701800-67710600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:67702800-67714600	Weak transcription	Small Intestine	intestine
28	chr12:67704400-67710600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:67704400-67712600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:67705600-67710600	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:67706200-67716400	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:67706600-67710600	Weak transcription	Left Ventricle	heart
33	chr12:67706600-67710600	Weak transcription	Thymus	Thymus
34	chr12:67706600-67710800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:67706600-67714200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:67706600-67716200	Weak transcription	Fetal Heart	heart
37	chr12:67706600-67720600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:67706800-67710600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:67706800-67710600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:67706800-67710800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:67706800-67712200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:67706800-67712200	Weak transcription	NHLF	lung
43	chr12:67706800-67712400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:67706800-67712400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:67706800-67712800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:67706800-67713200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:67706800-67713400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:67706800-67714400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:67706800-67714600	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:67706800-67714800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links