Variant report

Variant	rs538147
Chromosome Location	chr11:64129722-64129723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64125259..64126829-chr11:64127521..64129918,2	MCF-7	breast:
2	chr11:64014412..64017263-chr11:64129523..64131741,2	MCF-7	breast:
3	chr11:64083616..64085818-chr11:64128442..64130282,2	K562	blood:

Variant related genes	Relation type
ENSG00000126432	Chromatin interaction
ENSG00000162302	Chromatin interaction
ENSG00000256940	Chromatin interaction
ENSG00000257086	Chromatin interaction
ENSG00000173457	Chromatin interaction
ENSG00000173113	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10792430	1.00[YRI][hapmap]
rs10897487	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897488	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231757	0.82[AMR][1000 genomes]
rs11231770	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231771	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231772	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11542299	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11601651	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601860	0.85[AMR][1000 genomes]
rs11606015	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11606081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1199045	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1199046	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199047	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1662188	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1783521	0.82[AMR][1000 genomes]
rs17857342	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510066	0.87[ASW][hapmap];0.87[MEX][hapmap]
rs3132740	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474901	0.87[ASW][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs475032	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs479777	0.87[MEX][hapmap]
rs4930155	0.86[GIH][hapmap];0.87[MEX][hapmap]
rs499425	0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs508168	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs510372	0.98[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs516124	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519763	0.87[ASW][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs521950	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs527465	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs541207	0.89[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs542907	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs566128	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs574087	0.87[ASW][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs574835	0.86[AMR][1000 genomes]
rs600377	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs612448	0.87[ASW][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61886886	0.83[AMR][1000 genomes]
rs61886926	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs645078	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs646153	0.81[AMR][1000 genomes]
rs647152	0.83[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs663743	0.86[ASW][hapmap];0.82[MEX][hapmap]
rs694739	1.00[ASW][hapmap];0.87[MEX][hapmap]
rs72926005	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72926006	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs876064	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
6	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
7	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	237 gene(s)	inside rSNPs	diseases
8	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
9	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases
10	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
11	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
12	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
13	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
15	nsv818841	chr11:64097233-64129722	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
16	nsv897688	chr11:64107735-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv897689	chr11:64109118-64148420	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
18	nsv897690	chr11:64118422-64135298	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
19	nsv897691	chr11:64118422-64137875	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
20	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Leprosy	22019778	GWAS catalog
Primary biliary cirrhosis	21399635	GWAS catalog

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs538147	CHKA	cis	parietal	SCAN
rs538147	C11orf68	cis	cerebellum	SCAN
rs538147	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs538147	TAF6L	cis	parietal	SCAN
rs538147	FKBP2	cis	cerebellum	SCAN
rs538147	FKBP2	cis	parietal	SCAN
rs538147	CCDC88B	cis	lymphoblastoid	seeQTL
rs538147	CCDC88B	cis	cerebellum	SCAN
rs538147	CCS	cis	cerebellum	SCAN
rs538147	CCDC88B	cis	Cerebellum	GTEx
rs538147	CCDC88B	cis	multi-tissue	Pritchard
rs538147	C11orf68	cis	parietal	SCAN
rs538147	AP003774.1	cis	Whole Blood	GTEx
rs538147	PPP1CA	cis	parietal	SCAN
rs538147	CCDC88B	cis	Lymphoblastoid	GTEx
rs538147	SCGB2A2	cis	cerebellum	SCAN
rs538147	CCDC88B	cis	parietal	SCAN
rs538147	CCDC88	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64127400-64131600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:64127400-64136000	Weak transcription	Fetal Kidney	kidney
3	chr11:64127400-64140000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:64127400-64144400	Weak transcription	Psoas Muscle	Psoas
5	chr11:64127600-64132800	Weak transcription	Small Intestine	intestine
6	chr11:64127600-64139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:64127800-64130000	Genic enhancers	Fetal Thymus	thymus
8	chr11:64127800-64131600	Weak transcription	Right Atrium	heart
9	chr11:64127800-64132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:64127800-64137600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:64127800-64139800	Strong transcription	Fetal Intestine Small	intestine
12	chr11:64127800-64146800	Weak transcription	Fetal Heart	heart
13	chr11:64128000-64131000	Strong transcription	A549	lung
14	chr11:64128000-64131800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:64128000-64133800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:64128000-64135400	Strong transcription	Fetal Stomach	stomach
17	chr11:64128000-64135800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:64128000-64136200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:64128000-64138000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:64128000-64138200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:64128000-64138200	Strong transcription	Left Ventricle	heart
22	chr11:64128000-64138800	Strong transcription	Ovary	ovary
23	chr11:64128000-64139000	Strong transcription	Primary T cells from cord blood	blood
24	chr11:64128000-64139000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:64128000-64140000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:64128200-64131000	Strong transcription	Right Ventricle	heart
27	chr11:64128200-64131000	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:64128200-64131000	Strong transcription	NHLF	lung
29	chr11:64128200-64131200	Strong transcription	Pancreas	Pancrea
30	chr11:64128200-64131400	Strong transcription	Esophagus	oesophagus
31	chr11:64128200-64132400	Weak transcription	Brain Germinal Matrix	brain
32	chr11:64128200-64133400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:64128200-64134600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:64128200-64135600	Strong transcription	NH-A	brain
35	chr11:64128200-64135800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:64128200-64137000	Strong transcription	Colon Smooth Muscle	Colon
37	chr11:64128200-64138200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr11:64128200-64138400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr11:64128200-64138800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:64128200-64138800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:64128200-64139400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:64128200-64139600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:64128200-64139600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:64128200-64139800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:64128200-64140000	Strong transcription	Lung	lung
46	chr11:64128400-64130000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr11:64128400-64130400	Strong transcription	Colonic Mucosa	Colon
48	chr11:64128400-64131200	Strong transcription	HSMMtube	muscle
49	chr11:64128400-64131400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:64128400-64133800	Strong transcription	NHEK	skin

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