Variant report

Variant	rs11229087
Chromosome Location	chr11:57425699-57425700
allele	C/T
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	chr11:57335100..57336885-chr11:57425174..57426738,2	K562	blood:
2	chr11:57423095..57430151-chr11:57432283..57438412,24	K562	blood:
3	chr11:57425106..57425704-chr16:87425253..87426005,2	Hela-S3	cervix:
4	chr11:57423375..57427275-chr11:57433374..57437610,8	MCF-7	breast:
5	chr11:57423749..57426682-chr11:57508630..57510179,2	K562	blood:
6	chr11:57194115..57196219-chr11:57423627..57426056,2	K562	blood:
7	chr11:57414343..57418921-chr11:57423216..57427343,7	K562	blood:
8	chr11:57417074..57418991-chr11:57424889..57426673,2	K562	blood:
9	chr11:57424563..57426708-chr11:57434107..57436084,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140941	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000254732	Chromatin interaction
ENSG00000103264	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000134802	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000156599	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10896634	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11229115	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1267146	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12793139	0.91[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424752	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs2848445	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs479573	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs480933	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs483030	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs486995	0.84[ASN][1000 genomes]
rs491719	0.88[ASN][1000 genomes]
rs492131	0.88[ASN][1000 genomes]
rs501054	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs501738	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs503037	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs504311	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs507946	0.82[ASN][1000 genomes]
rs509564	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs511708	0.88[ASN][1000 genomes]
rs515939	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs517638	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs518804	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs523985	0.88[ASN][1000 genomes]
rs527140	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs530094	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs536673	0.88[ASN][1000 genomes]
rs537627	0.88[ASN][1000 genomes]
rs540234	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs541245	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs544446	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs549022	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs549279	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs558653	0.88[ASN][1000 genomes]
rs567017	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs577741	0.88[ASN][1000 genomes]
rs581217	0.82[ASN][1000 genomes]
rs594233	0.84[ASN][1000 genomes]
rs604094	0.84[ASN][1000 genomes]
rs604344	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs608648	0.84[ASN][1000 genomes]
rs609596	0.81[ASN][1000 genomes]
rs612688	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs61888873	0.88[ASN][1000 genomes]
rs61888880	0.88[ASN][1000 genomes]
rs624759	0.82[ASN][1000 genomes]
rs628100	0.83[ASN][1000 genomes]
rs636807	0.81[ASN][1000 genomes]
rs638864	0.84[ASN][1000 genomes]
rs640767	0.84[ASN][1000 genomes]
rs645097	0.83[ASN][1000 genomes]
rs647264	0.84[ASN][1000 genomes]
rs656227	0.84[ASN][1000 genomes]
rs658183	0.84[ASN][1000 genomes]
rs666021	0.81[ASN][1000 genomes]
rs669433	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs669950	0.89[ASN][1000 genomes]
rs675154	0.84[ASN][1000 genomes]
rs7108113	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11229087	SPRYD5	cis	cerebellum	SCAN
rs11229087	OR4C11	cis	cerebellum	SCAN
rs11229087	YPEL4	cis	lymphoblastoid	seeQTL
rs11229087	TNKS1BP1	cis	parietal	SCAN
rs11229087	MED19	cis	cerebellum	SCAN
rs11229087	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57424400-57425800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr11:57424400-57426000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:57424400-57426000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr11:57424400-57426000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:57424400-57426000	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr11:57424400-57426000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr11:57424400-57426400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:57424600-57425800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:57424600-57425800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:57424600-57425800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:57424600-57425800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr11:57424600-57425800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:57424600-57425800	Active TSS	Aorta	Aorta
14	chr11:57424600-57425800	Active TSS	Esophagus	oesophagus
15	chr11:57424600-57425800	Active TSS	Fetal Intestine Large	intestine
16	chr11:57424600-57425800	Active TSS	Fetal Intestine Small	intestine
17	chr11:57424600-57425800	Active TSS	Left Ventricle	heart
18	chr11:57424600-57425800	Active TSS	Pancreas	Pancrea
19	chr11:57424600-57425800	Active TSS	HSMMtube	muscle
20	chr11:57424600-57426000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:57424600-57426000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr11:57424600-57426000	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr11:57424600-57426000	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr11:57424600-57426000	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr11:57424600-57426000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr11:57424600-57426000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr11:57424600-57426000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:57424600-57426000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:57424600-57426000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:57424600-57426000	Active TSS	Colonic Mucosa	Colon
31	chr11:57424600-57426000	Active TSS	Ovary	ovary
32	chr11:57424600-57426000	Active TSS	Psoas Muscle	Psoas
33	chr11:57424600-57426000	Active TSS	Right Atrium	heart
34	chr11:57424600-57426000	Active TSS	Right Ventricle	heart
35	chr11:57424600-57426000	Active TSS	A549	lung
36	chr11:57424600-57426000	Bivalent/Poised TSS	HepG2	liver
37	chr11:57424600-57426000	Active TSS	NHEK	skin
38	chr11:57424600-57426200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:57424800-57425800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:57424800-57425800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:57424800-57425800	Active TSS	Muscle Satellite Cultured Cells	--
42	chr11:57424800-57425800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:57424800-57425800	Active TSS	Gastric	stomach
44	chr11:57424800-57425800	Active TSS	Lung	lung
45	chr11:57424800-57425800	Active TSS	Small Intestine	intestine
46	chr11:57424800-57425800	Active TSS	NHDF-Ad	bronchial
47	chr11:57424800-57426000	Active TSS	H1 Cell Line	embryonic stem cell
48	chr11:57424800-57426000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:57424800-57426000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:57424800-57426000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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