Variant report

Variant	rs12712981
Chromosome Location	chr2:47189642-47189643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47188627..47191352-chr2:48004786..48007353,2	MCF-7	breast:
2	chr2:47166769..47171325-chr2:47189456..47193821,11	MCF-7	breast:
3	chr2:47187193..47190243-chr2:47190337..47193752,4	MCF-7	breast:
4	chr2:47164675..47170526-chr2:47188235..47196918,12	MCF-7	breast:
5	chr2:47188341..47190485-chr2:47209167..47212158,2	MCF-7	breast:
6	chr2:47188688..47191664-chr2:47211239..47213547,2	K562	blood:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10183233	0.83[CHB][hapmap]
rs10495941	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779934	0.81[JPT][hapmap]
rs11125103	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125104	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11125105	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1122516	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11685461	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12053441	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712982	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712984	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13002842	0.87[CEU][hapmap]
rs13014374	0.89[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1865261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278449	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278450	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28434195	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28694585	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952857	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4953438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544943	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6544944	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6713810	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6745836	0.81[EUR][1000 genomes]
rs735887	0.88[ASN][1000 genomes]
rs735888	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7557193	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560371	0.83[CHB][hapmap]
rs7602813	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs892380	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47173000-47191800	Weak transcription	Fetal Brain Male	brain
3	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47176400-47192600	Strong transcription	Dnd41	blood
5	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
7	chr2:47177600-47190000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr2:47177600-47191200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:47178400-47192800	Strong transcription	Thymus	Thymus
10	chr2:47178600-47189800	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:47178800-47190000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:47178800-47191400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:47179000-47191000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:47179000-47192800	Strong transcription	Primary T cells from cord blood	blood
15	chr2:47179200-47195000	Strong transcription	Fetal Thymus	thymus
16	chr2:47179400-47191400	Strong transcription	Primary hematopoietic stem cells	blood
17	chr2:47179400-47192200	Strong transcription	Primary B cells from cord blood	blood
18	chr2:47179400-47192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:47179400-47193800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:47181200-47192200	Strong transcription	GM12878-XiMat	blood
21	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:47182600-47189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:47182600-47190400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:47183000-47189800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:47183000-47189800	Weak transcription	K562	blood
26	chr2:47183000-47192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:47183000-47195000	Weak transcription	Small Intestine	intestine
28	chr2:47183200-47190400	Strong transcription	Osteobl	bone
29	chr2:47183400-47191000	Strong transcription	NHLF	lung
30	chr2:47183400-47191200	Strong transcription	HSMM	muscle
31	chr2:47183400-47192200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:47183400-47192600	Strong transcription	Fetal Intestine Large	intestine
33	chr2:47183400-47193400	Strong transcription	Fetal Intestine Small	intestine
34	chr2:47183600-47190000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:47183600-47190000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:47183600-47190200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:47183600-47190600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:47183600-47190800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:47183800-47189800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:47184200-47194400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:47184600-47190000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:47184600-47197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:47184600-47205000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:47184800-47190800	Weak transcription	HUVEC	blood vessel
45	chr2:47185000-47206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:47185400-47189800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:47185400-47191000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:47185400-47205800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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