Variant report

Variant	rs694739
Chromosome Location	chr11:64097233-64097234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr11:64096994-64097281	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64012363..64015118-chr11:64095317..64097895,3	MCF-7	breast:
2	chr11:64052931..64055348-chr11:64095161..64098427,3	MCF-7	breast:
3	chr11:64006100..64009452-chr11:64096947..64099274,3	K562	blood:

Variant related genes	Relation type
ENSG00000236935	TF binding region
ENSG00000173486	Chromatin interaction
ENSG00000256940	Chromatin interaction
ENSG00000173264	Chromatin interaction
ENSG00000173457	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10897488	1.00[ASW][hapmap];0.83[MEX][hapmap]
rs11231757	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601860	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11606081	1.00[ASW][hapmap]
rs1199045	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1199046	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1783521	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2510066	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474901	0.87[ASW][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs479552	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs479777	0.84[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs499425	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508168	1.00[ASW][hapmap];0.83[MEX][hapmap]
rs510372	0.83[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs516124	1.00[ASW][hapmap];0.87[MEX][hapmap]
rs519763	0.87[ASW][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs538147	1.00[ASW][hapmap];0.87[MEX][hapmap]
rs542907	0.85[AFR][1000 genomes]
rs566128	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs574087	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs574835	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs600377	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs612448	0.87[ASW][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs61886886	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627425	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs645078	1.00[ASW][hapmap];0.83[MEX][hapmap]
rs646153	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs647152	0.81[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs663743	0.86[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs887314	0.80[AMR][1000 genomes]
rs915987	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
10	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
11	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	nsv555192	chr11:64097233-64111928	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	n/a
20	nsv818840	chr11:64097233-64125142	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
21	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

Variant related diseases (count:2)

Disease	PMID	Source
Alopecia areata	20596022	GWAS catalog
Crohn's disease	21102463	GWAS catalog

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs694739	SCGB2A2	cis	cerebellum	SCAN
rs694739	CCDC88	cis	multi-tissue	Pritchard
rs694739	CCDC88B	cis	cerebellum	SCAN
rs694739	C11orf68	cis	cerebellum	SCAN
rs694739	FKBP2	cis	cerebellum	SCAN
rs694739	CCDC88B	cis	Esophagus Muscularis	GTEx
rs694739	PPP1CA	cis	parietal	SCAN
rs694739	TAF6L	cis	parietal	SCAN
rs694739	CCDC88B	cis	Esophagus Mucosa	GTEx
rs694739	CCDC88B	cis	lymphoblastoid	seeQTL
rs694739	CCDC88B	cis	multi-tissue	Pritchard
rs694739	CCS	cis	cerebellum	SCAN
rs694739	MALAT1	cis	cerebellum	SCAN
rs694739	AP003774.1	cis	Whole Blood	GTEx
rs694739	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs694739	CCDC88B	cis	Cerebellum	GTEx
rs694739	FKBP2	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64086800-64099000	Weak transcription	Small Intestine	intestine
2	chr11:64087000-64099000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:64087000-64099000	Weak transcription	HSMM	muscle
4	chr11:64087000-64108200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:64087200-64098800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:64087200-64099000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:64087200-64099000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:64087400-64099000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:64087400-64099000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:64089200-64098600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:64089400-64106800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:64090000-64098600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr11:64090200-64099400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:64090600-64098400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:64090600-64098800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:64090600-64099000	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:64090600-64099000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:64090600-64099200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:64090600-64099200	Weak transcription	Brain Angular Gyrus	brain
20	chr11:64090800-64098600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr11:64091000-64098400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:64091000-64098600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:64091000-64098800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:64091000-64099000	Weak transcription	Fetal Lung	lung
25	chr11:64091000-64099200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:64091000-64099200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:64091200-64099200	Weak transcription	Brain Anterior Caudate	brain
28	chr11:64091200-64099200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:64091400-64098600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:64091600-64098000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:64091600-64098400	Weak transcription	K562	blood
32	chr11:64091600-64098600	Weak transcription	Primary B cells from cord blood	blood
33	chr11:64091600-64099000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:64091600-64099000	Weak transcription	Gastric	stomach
35	chr11:64091600-64099400	Weak transcription	Thymus	Thymus
36	chr11:64091600-64106400	Weak transcription	Primary T cells from cord blood	blood
37	chr11:64091800-64098200	Weak transcription	Spleen	Spleen
38	chr11:64092000-64098400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:64092000-64098400	Weak transcription	Esophagus	oesophagus
40	chr11:64092600-64098400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:64092600-64099000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:64093000-64098600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:64093200-64098400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:64094000-64097800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr11:64095200-64099200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:64095400-64098800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:64096200-64097600	Enhancers	Adipose Nuclei	Adipose
48	chr11:64096200-64098400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr11:64096400-64097400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:64096400-64097400	Enhancers	Duodenum Mucosa	Duodenum

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