Variant report

Variant	rs11231726
Chromosome Location	chr11:63987339-63987340
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	POLR2A	chr11:63986470-63988736	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:63986414-63987353	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:63987205-63987404	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:63986184-63988706	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:63987221-63987372	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:63986146-63988985	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:63985776-63988920	K562	blood:	n/a	n/a
8	POLR2A	chr11:63986896-63987379	K562	blood:	n/a	n/a
9	POLR2A	chr11:63987177-63988623	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr11:63986259-63987634	K562	blood:	n/a	n/a
11	POLR2A	chr11:63985761-63989003	K562	blood:	n/a	n/a
12	POLR2A	chr11:63986566-63988071	GM18951	blood:	n/a	n/a
13	POLR2A	chr11:63986440-63987343	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:63986634-63987829	K562	blood:	n/a	n/a
15	POLR2A	chr11:63986104-63988898	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:63985910-63989071	GM12891	blood:	n/a	n/a
17	POLR2A	chr11:63986773-63987957	K562	blood:	n/a	n/a
18	POLR2A	chr11:63986353-63988901	K562	blood:	n/a	n/a
19	POLR2A	chr11:63986463-63988020	GM19193	blood:	n/a	n/a
20	POLR2A	chr11:63987070-63987357	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr11:63987224-63987629	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr11:63985577-63989019	GM12892	blood:	n/a	n/a
23	POLR2A	chr11:63986336-63987402	GM19099	blood:	n/a	n/a
24	POLR2A	chr11:63987023-63987806	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:63985730-63989094	K562	blood:	n/a	n/a
26	POLR2A	chr11:63986618-63987393	HL-60	blood:	n/a	n/a
27	POLR2A	chr11:63986226-63988808	GM18505	blood:	n/a	n/a
28	POLR2A	chr11:63987326-63987782	GM12892	blood:	n/a	n/a
29	POLR2A	chr11:63986084-63987852	K562	blood:	n/a	n/a
30	POLR2A	chr11:63986407-63988084	GM12892	blood:	n/a	n/a
31	POLR2A	chr11:63986272-63988830	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
FERMT3	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1011219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231710	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231713	0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11600628	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600667	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11604083	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11605193	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11605856	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607903	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12417635	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12419038	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17773078	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2005272	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2096706	0.82[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2186572	0.88[EUR][1000 genomes]
rs3862371	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55942618	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55970968	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56207008	0.91[EUR][1000 genomes]
rs56311067	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57021319	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57831436	0.84[AMR][1000 genomes]
rs58779949	0.84[AMR][1000 genomes]
rs60394481	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs646384	0.80[TSI][hapmap]
rs7103915	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7109921	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122408	0.81[EUR][1000 genomes]
rs7123026	0.89[EUR][1000 genomes]
rs734762	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7941773	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947939	0.82[CHD][hapmap];0.84[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
11	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
12	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
13	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
14	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
15	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
16	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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 target site	212 gene(s)	inside rSNPs	diseases
17	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
18	nsv468595	chr11:63953121-64027888	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
19	nsv555187	chr11:63953121-64027888	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
20	nsv897667	chr11:63964657-64078380	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
21	nsv897668	chr11:63964657-64085298	Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
22	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
23	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
24	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
25	nsv541061	chr11:63970174-64010995	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
26	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
27	nsv897672	chr11:63979643-64082807	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS 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 target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11231726	RBM14	cis	cerebellum	SCAN
rs11231726	FKBP2	cis	parietal	SCAN
rs11231726	ESRRA	cis	cerebellum	SCAN
rs11231726	RAB1B	cis	cerebellum	SCAN
rs11231726	MALAT1	cis	cerebellum	SCAN
rs11231726	NAA40	cis	cerebellum	SCAN
rs11231726	CCDC88B	cis	cerebellum	SCAN
rs11231726	ANKRD13D	cis	cerebellum	SCAN
rs11231726	NUDT22	Cis_1M	lymphoblastoid	RTeQTL
rs11231726	FLRT1	cis	cerebellum	SCAN
rs11231726	RCE1	cis	cerebellum	SCAN
rs11231726	CCS	cis	cerebellum	SCAN
rs11231726	FKBP2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63971600-63992800	Weak transcription	Fetal Kidney	kidney
2	chr11:63972000-63990000	Weak transcription	Ovary	ovary
3	chr11:63973200-63987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:63973600-63993000	Weak transcription	Aorta	Aorta
5	chr11:63974800-63987600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:63975000-63988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:63975200-63992600	Weak transcription	Brain Angular Gyrus	brain
8	chr11:63975400-63990200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:63975600-63992400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:63975600-63992600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:63975600-63992600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:63975600-63992800	Weak transcription	Fetal Lung	lung
13	chr11:63975800-63988000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:63975800-63990200	Weak transcription	Psoas Muscle	Psoas
15	chr11:63975800-63990400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:63975800-63992400	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:63975800-63992600	Weak transcription	Left Ventricle	heart
18	chr11:63975800-63992600	Weak transcription	Osteobl	bone
19	chr11:63975800-63993000	Weak transcription	Small Intestine	intestine
20	chr11:63976200-63992400	Strong transcription	Fetal Intestine Small	intestine
21	chr11:63976400-63987600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:63976400-63992800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:63976600-63987400	Weak transcription	Adipose Nuclei	Adipose
24	chr11:63976600-63992600	Weak transcription	HUVEC	blood vessel
25	chr11:63976800-63992800	Weak transcription	Brain Substantia Nigra	brain
26	chr11:63977200-63991600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:63977400-63991800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr11:63977400-63992000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:63977400-63992000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:63977400-63992200	Strong transcription	Fetal Thymus	thymus
31	chr11:63977600-63991800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr11:63977800-63991400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:63977800-63991400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:63977800-63991600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:63978600-63990800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:63979600-63987600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:63979800-63987400	Weak transcription	Esophagus	oesophagus
38	chr11:63979800-63992600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr11:63980000-63987600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:63980000-63991400	Weak transcription	A549	lung
41	chr11:63980200-63987600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:63980200-63987600	Weak transcription	Fetal Brain Female	brain
43	chr11:63980200-63990200	Weak transcription	HSMM	muscle
44	chr11:63980200-63991600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr11:63981800-63988800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr11:63982200-63992400	Strong transcription	Thymus	Thymus
47	chr11:63982600-63988200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:63982800-63988000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:63983000-63987400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:63983000-63992400	Strong transcription	Primary neutrophils fromperipheralblood	blood

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