Variant report

Variant	rs12222675
Chromosome Location	chr11:58905336-58905337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58904183..58908174-chr11:58910132..58913359,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166801	Chromatin interaction
ENSG00000245571	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048374	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10896948	1.00[CEU][hapmap]
rs10896954	1.00[CEU][hapmap]
rs11229810	0.84[CHB][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229821	1.00[EUR][1000 genomes]
rs11229825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs11229829	1.00[EUR][1000 genomes]
rs11229831	1.00[EUR][1000 genomes]
rs11229832	1.00[EUR][1000 genomes]
rs11229835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229838	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229842	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229843	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229844	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11229858	0.91[ASN][1000 genomes]
rs11229862	0.81[ASN][1000 genomes]
rs11229871	1.00[CEU][hapmap]
rs11229891	1.00[CEU][hapmap]
rs11229905	1.00[CEU][hapmap]
rs12221768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12223473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12225532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12275736	1.00[CEU][hapmap]
rs17153381	1.00[EUR][1000 genomes]
rs2154626	1.00[EUR][1000 genomes]
rs2154627	1.00[EUR][1000 genomes]
rs2154964	1.00[EUR][1000 genomes]
rs2154965	1.00[EUR][1000 genomes]
rs35732637	1.00[EUR][1000 genomes]
rs55742277	1.00[EUR][1000 genomes]
rs56349021	1.00[EUR][1000 genomes]
rs57969871	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58277547	1.00[ASN][1000 genomes]
rs60519524	1.00[EUR][1000 genomes]
rs60795438	1.00[EUR][1000 genomes]
rs60883299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951382	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58875200-58909600	Weak transcription	Stomach Mucosa	stomach
2	chr11:58875400-58909600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:58893800-58909600	Weak transcription	Fetal Brain Male	brain
4	chr11:58899000-58909600	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:58899600-58909600	Weak transcription	Aorta	Aorta
6	chr11:58899800-58909600	Weak transcription	Colonic Mucosa	Colon
7	chr11:58899800-58909800	Weak transcription	Gastric	stomach
8	chr11:58899800-58909800	Weak transcription	Small Intestine	intestine
9	chr11:58899800-58910000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:58900000-58909400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:58900000-58909400	Weak transcription	A549	lung
12	chr11:58900000-58909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:58900000-58909600	Weak transcription	Fetal Lung	lung
14	chr11:58900000-58910000	Weak transcription	Spleen	Spleen
15	chr11:58900200-58905400	Weak transcription	Lung	lung
16	chr11:58900600-58909400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:58901200-58909600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:58901400-58909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:58901400-58909800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:58901800-58909000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:58902200-58909000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:58902400-58909400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:58902800-58905400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:58902800-58908800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:58902800-58909000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:58903000-58909200	Weak transcription	HSMM	muscle
27	chr11:58903000-58909400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:58903000-58909400	Weak transcription	NHDF-Ad	bronchial
29	chr11:58903200-58905400	Enhancers	Fetal Intestine Large	intestine
30	chr11:58903200-58905800	Genic enhancers	Fetal Intestine Small	intestine
31	chr11:58903600-58909600	Weak transcription	Pancreas	Pancrea
32	chr11:58903600-58909800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:58903800-58905400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:58903800-58905400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:58903800-58905600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:58903800-58908600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:58903800-58908600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:58903800-58908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr11:58903800-58908600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:58903800-58908600	Weak transcription	Brain Angular Gyrus	brain
41	chr11:58903800-58909000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr11:58903800-58909000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr11:58903800-58909000	Weak transcription	GM12878-XiMat	blood
44	chr11:58903800-58909200	Weak transcription	Hela-S3	cervix
45	chr11:58903800-58909200	Weak transcription	HMEC	breast
46	chr11:58903800-58909400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:58903800-58909400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:58903800-58909400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:58903800-58909400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:58903800-58909400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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