Variant report

Variant	rs11231141
Chromosome Location	chr11:62326265-62326266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62325962-62326959	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:62325823-62326969	HL-60	blood:	n/a	n/a
3	POLR2A	chr11:62325927-62327033	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr11:62325861-62326298	U87	brain:	n/a	n/a
5	ZNF384	chr11:62325484-62326690	GM12878	blood:	n/a	n/a
6	PML	chr11:62325661-62326463	GM12878	blood:	n/a	n/a
7	POLR2A	chr11:62326121-62326563	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:62326121-62326559	GM12891	blood:	n/a	n/a
9	POLR2A	chr11:62323618-62327355	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:62326194-62326427	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:62326097-62326482	GM12891	blood:	n/a	n/a
12	POLR2A	chr11:62325774-62326474	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr11:62326224-62326429	GM12878	blood:	n/a	n/a
14	MTA3	chr11:62325781-62326507	GM12878	blood:	n/a	n/a
15	POLR2A	chr11:62326092-62326423	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr11:62326241-62326504	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:62326046-62326592	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:62326193-62326503	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr11:62322648-62329156	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr11:62325653-62328531	K562	blood:	n/a	n/a
21	POLR2A	chr11:62326153-62326362	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr11:62326121-62326403	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:62326069-62326608	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:62326102-62326547	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:62325159-62326777	GM12892	blood:	n/a	n/a
26	POLR2A	chr11:62325835-62326542	K562	blood:	n/a	n/a
27	POLR2A	chr11:62322635-62329744	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr11:62325465-62326644	K562	blood:	n/a	n/a
29	POLR2A	chr11:62326172-62326465	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:62323391-62326700	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr11:62326177-62326387	MCF-7	breast:	n/a	n/a
32	POLR2A	chr11:62323448-62326435	K562	blood:	n/a	n/a
33	POLR2A	chr11:62326247-62326408	HepG2	liver:	n/a	n/a
34	POLR2A	chr11:62326158-62326367	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:62326154-62326469	HCT-116	colon:	n/a	n/a
36	POLR2A	chr11:62326137-62326417	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr11:62326182-62326450	HepG2	liver:	n/a	n/a
38	POLR2A	chr11:62326013-62326403	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr11:62326105-62326499	GM12892	blood:	n/a	n/a
40	POLR2A	chr11:62326136-62326338	A549	lung:	n/a	n/a
41	POLR2A	chr11:62325956-62326430	K562	blood:	n/a	n/a
42	POLR2A	chr11:62326197-62326545	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr11:62326170-62326420	GM12878	blood:	n/a	n/a
44	POLR2A	chr11:62325861-62326423	U87	brain:	n/a	n/a
45	POLR2A	chr11:62326009-62326444	HepG2	liver:	n/a	n/a
46	POLR2A	chr11:62326033-62326393	HCT-116	colon:	n/a	n/a
47	POLR2A	chr11:62326016-62327129	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62325930..62327959-chr11:62493506..62496408,2	K562	blood:
2	chr11:62325310..62327831-chr11:62339551..62341590,4	K562	blood:
3	chr11:62323837..62326900-chr11:62339205..62341755,6	K562	blood:

No data

Variant related genes	Relation type
AHNAK	TF binding region
ENSG00000162222	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000214753	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1061093	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231137	0.97[ASN][1000 genomes]
rs11231138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231145	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231151	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231152	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11231154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231155	0.90[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231161	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11231176	1.00[JPT][hapmap]
rs11553576	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs12049914	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12223627	0.80[ASN][1000 genomes]
rs12225213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12226821	0.80[ASN][1000 genomes]
rs12808829	0.84[EUR][1000 genomes]
rs17773169	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1801144	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2428548	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2428549	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2428551	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2509961	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2509967	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2509982	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2512562	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2512563	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2516633	0.88[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2516634	0.89[EUR][1000 genomes]
rs2849030	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2849031	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs34065644	0.80[ASN][1000 genomes]
rs34894392	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35156678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs35587183	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35880596	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58720921	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60098285	1.00[ASN][1000 genomes]
rs61296092	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124057	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71490390	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71490392	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71490394	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72927213	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7928833	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7937146	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7942154	1.00[ASN][1000 genomes]
rs7942991	0.89[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7943191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
5	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	esv1801128	chr11:62276347-62329897	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
7	esv1831183	chr11:62276347-62329897	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' 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	245 gene(s)	inside rSNPs	diseases
9	nsv347	chr11:62297068-62338927	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
10	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	122 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11231141	EML3	cis	Esophagus Mucosa	GTEx
rs11231141	SLC22A25	cis	parietal	SCAN
rs11231141	C11orf48	cis	cerebellum	SCAN
rs11231141	TUT1	cis	parietal	SCAN
rs11231141	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs11231141	EML3	cis	Whole Blood	GTEx
rs11231141	ROM1	cis	Thyroid	GTEx
rs11231141	CFL1	cis	parietal	SCAN
rs11231141	EEF1G	cis	multi-tissue	Pritchard
rs11231141	EML3	cis	cerebellum	SCAN
rs11231141	MTA2	cis	Esophagus Mucosa	GTEx
rs11231141	SCYL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62319000-62326600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr11:62322000-62326400	Genic enhancers	Fetal Intestine Small	intestine
3	chr11:62322400-62328000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:62322400-62328200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:62322400-62340000	Strong transcription	Fetal Brain Female	brain
6	chr11:62322600-62331200	Weak transcription	Ovary	ovary
7	chr11:62324200-62329000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr11:62324400-62328200	Genic enhancers	HSMM	muscle
9	chr11:62324400-62328600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:62324400-62328800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:62324600-62326400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr11:62324600-62327400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:62324600-62327600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:62324600-62327600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
15	chr11:62324600-62327800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
16	chr11:62324600-62327800	Strong transcription	Brain Substantia Nigra	brain
17	chr11:62324600-62328000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:62324600-62331600	Genic enhancers	Placenta	Placenta
19	chr11:62324800-62326400	Genic enhancers	Fetal Thymus	thymus
20	chr11:62324800-62327800	Strong transcription	Liver	Liver
21	chr11:62324800-62328200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:62324800-62329000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:62324800-62329600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr11:62324800-62330000	Genic enhancers	HMEC	breast
25	chr11:62324800-62333600	Weak transcription	Small Intestine	intestine
26	chr11:62324800-62338800	Strong transcription	Brain Germinal Matrix	brain
27	chr11:62324800-62339600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:62325000-62326400	Enhancers	Stomach Mucosa	stomach
29	chr11:62325000-62326600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:62325000-62326600	Weak transcription	Fetal Heart	heart
31	chr11:62325000-62326800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:62325000-62327200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:62325000-62327200	Weak transcription	Right Atrium	heart
34	chr11:62325000-62327400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:62325000-62327600	Strong transcription	Rectal Smooth Muscle	rectum
36	chr11:62325000-62327800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:62325000-62327800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:62325000-62327800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:62325000-62327800	Strong transcription	Brain Hippocampus Middle	brain
40	chr11:62325000-62328000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:62325000-62328400	Genic enhancers	Hela-S3	cervix
42	chr11:62325000-62329000	Strong transcription	Fetal Stomach	stomach
43	chr11:62325000-62331200	Weak transcription	Psoas Muscle	Psoas
44	chr11:62325000-62331800	Genic enhancers	A549	lung
45	chr11:62325000-62338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:62325000-62338800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:62325200-62326800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:62325200-62326800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr11:62325200-62327000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr11:62325200-62327400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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