Variant report

Variant	rs7476
Chromosome Location	chr11:46342834-46342835
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46337540..46339724-chr11:46341786..46344152,2	K562	blood:
2	chr11:46140061..46142521-chr11:46342623..46344469,2	MCF-7	breast:
3	chr11:46340260..46343064-chr11:46368251..46371129,2	MCF-7	breast:
4	chr11:46315406..46317942-chr11:46339600..46342973,3	K562	blood:
5	chr11:46341667..46343231-chr11:46348758..46351326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135365	Chromatin interaction
ENSG00000157613	Chromatin interaction
ENSG00000149091	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10838596	1.00[ASW][hapmap];0.96[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];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11038860	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11038866	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11038871	0.83[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs12273290	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17787804	0.93[MEX][hapmap];0.93[TSI][hapmap]
rs3802890	0.83[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs4565870	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6485672	0.88[JPT][hapmap]
rs6485673	0.88[JPT][hapmap]
rs6485674	0.88[JPT][hapmap]
rs7949282	0.83[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs7949371	0.83[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][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	nsv554201	chr11:46281835-46422686	Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv825867	chr11:46303184-46425613	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1797501	chr11:46315437-46402521	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv1811345	chr11:46317062-46438072	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7476	TP53I11	cis	cerebellum	SCAN
rs7476	OR4X2	cis	parietal	SCAN
rs7476	CD82	cis	cerebellum	SCAN
rs7476	OR52B6	trans	cerebellum	SCAN
rs7476	ACP2	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46319400-46346000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:46322000-46345000	Weak transcription	Small Intestine	intestine
3	chr11:46329000-46344000	Strong transcription	Fetal Intestine Large	intestine
4	chr11:46329200-46346800	Weak transcription	Fetal Kidney	kidney
5	chr11:46330200-46349400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:46330600-46344800	Strong transcription	Fetal Intestine Small	intestine
7	chr11:46330600-46345000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:46330600-46346200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:46330600-46348200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:46330600-46348800	Strong transcription	Fetal Stomach	stomach
11	chr11:46330800-46344600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:46330800-46348200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:46331200-46344200	Strong transcription	Osteobl	bone
14	chr11:46331400-46344800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:46331400-46345000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:46331600-46343800	Strong transcription	NHLF	lung
17	chr11:46331600-46345000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:46331800-46344000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:46332000-46344600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:46332200-46344200	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr11:46334400-46346000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:46335800-46345000	Strong transcription	NH-A	brain
23	chr11:46336400-46345200	Strong transcription	HSMM	muscle
24	chr11:46336600-46344000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:46336600-46344800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr11:46336800-46343000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:46336800-46346800	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:46337000-46343800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr11:46337000-46344600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:46337200-46343800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:46337200-46344200	Strong transcription	NHDF-Ad	bronchial
32	chr11:46337400-46344200	Strong transcription	HSMMtube	muscle
33	chr11:46337600-46343600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:46337600-46344000	Strong transcription	Gastric	stomach
35	chr11:46337600-46346000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr11:46338800-46343200	Strong transcription	Pancreas	Pancrea
37	chr11:46338800-46351400	Weak transcription	Fetal Heart	heart
38	chr11:46340200-46343000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:46340200-46348200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:46340600-46348400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:46340600-46349000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:46340800-46343600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:46340800-46344000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:46340800-46344000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr11:46340800-46344000	Strong transcription	Left Ventricle	heart
46	chr11:46340800-46344800	Weak transcription	Stomach Mucosa	stomach
47	chr11:46340800-46345200	Enhancers	Primary B cells from cord blood	blood
48	chr11:46340800-46346800	Weak transcription	Fetal Lung	lung
49	chr11:46341000-46343000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:46341000-46343400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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