Variant report

Variant	rs11229840
Chromosome Location	chr11:58910926-58910927
allele	G/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	chr11:58909956-58911022	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:58909874-58910956	GM19193	blood:	n/a	n/a
3	POLR2A	chr11:58909884-58911111	GM18505	blood:	n/a	n/a
4	RFX5	chr11:58909614-58911319	Hela-S3	cervix:	n/a	chr11:58910569-58910578
5	POLR2A	chr11:58909921-58911125	HepG2	liver:	n/a	n/a
6	BCL3	chr11:58909910-58911009	A549	lung:	n/a	chr11:58910712-58910721
7	POLR2A	chr11:58909722-58913181	GM12891	blood:	n/a	n/a
8	MAX	chr11:58909957-58910956	H1-hESC	embryonic stem cell:	n/a	n/a
9	KAP1	chr11:58910304-58910980	U2OS	brain:	n/a	n/a
10	MAX	chr11:58909879-58910939	GM12878	blood:	n/a	n/a
11	TAF1	chr11:58909859-58911072	H1-hESC	embryonic stem cell:	n/a	n/a
12	RCOR1	chr11:58909714-58910991	K562	blood:	n/a	n/a
13	POLR2A	chr11:58909840-58911176	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr11:58909834-58910928	GM12891	blood:	n/a	chr11:58910713-58910722 chr11:58910713-58910722
15	STAT5A	chr11:58909875-58910984	GM12878	blood:	n/a	chr11:58910702-58910714 chr11:58910357-58910368 chr11:58910708-58910719
16	POLR2A	chr11:58909881-58911018	GM12892	blood:	n/a	n/a
17	POLR2A	chr11:58909748-58911031	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:58909836-58911024	GM12878	blood:	n/a	n/a
19	GATA3	chr11:58910481-58911003	T-47D	breast:	n/a	n/a
20	RELA	chr11:58909699-58911035	GM19099	blood:	n/a	chr11:58910713-58910722 chr11:58910713-58910722
21	NRF1	chr11:58909954-58911078	GM12878	blood:	n/a	n/a
22	GABPA	chr11:58909821-58910983	MCF-7	breast:	n/a	n/a
23	PAX5	chr11:58909956-58910947	GM12878	blood:	n/a	n/a
24	EP300	chr11:58909971-58910927	T-47D	breast:	n/a	chr11:58910304-58910313
25	MAX	chr11:58909777-58910986	A549	lung:	n/a	n/a
26	MTA3	chr11:58909680-58910980	GM12878	blood:	n/a	n/a
27	USF2	chr11:58910446-58911123	Hela-S3	cervix:	n/a	n/a
28	E2F6	chr11:58909909-58910964	H1-hESC	embryonic stem cell:	n/a	chr11:58910568-58910577 chr11:58910504-58910513
29	BCLAF1	chr11:58909734-58910936	GM12878	blood:	n/a	chr11:58910712-58910721
30	IRF1	chr11:58909987-58910991	K562	blood:	n/a	chr11:58910357-58910371 chr11:58910357-58910370 chr11:58910358-58910372 chr11:58910364-58910381 chr11:58910357-58910368 chr11:58910356-58910367 chr11:58910354-58910371 chr11:58910568-58910577 chr11:58910352-58910369 chr11:58910357-58910370 chr11:58910358-58910368 chr11:58910352-58910373 chr11:58910362-58910382 chr11:58910357-58910370 chr11:58910357-58910369 chr11:58910356-58910376 chr11:58910358-58910375
31	POLR2A	chr11:58909885-58910978	MCF-7	breast:	n/a	n/a
32	RUNX3	chr11:58909909-58911034	GM12878	blood:	n/a	n/a
33	RCOR1	chr11:58909604-58911055	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr11:58909554-58910929	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:58909802-58911072	Hela-S3	cervix:	n/a	n/a
36	TBP	chr11:58910026-58910995	H1-hESC	embryonic stem cell:	n/a	n/a
37	ZEB1	chr11:58909880-58911007	HepG2	liver:	n/a	n/a
38	POLR2A	chr11:58909979-58911672	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr11:58909833-58911003	GM19099	blood:	n/a	n/a
40	NFIC	chr11:58909706-58910982	GM12878	blood:	n/a	n/a
41	IRF1	chr11:58909985-58912557	K562	blood:	n/a	chr11:58910357-58910371 chr11:58912180-58912194 chr11:58910357-58910370 chr11:58911818-58911829 chr11:58911816-58911830 chr11:58910358-58910372 chr11:58910364-58910381 chr11:58910357-58910368 chr11:58910356-58910367 chr11:58910354-58910371 chr11:58910568-58910577 chr11:58910352-58910369 chr11:58912184-58912194 chr11:58912184-58912195 chr11:58910357-58910370 chr11:58912021-58912030 chr11:58910358-58910368 chr11:58912183-58912195 chr11:58910352-58910373 chr11:58910362-58910382 chr11:58912184-58912198 chr11:58910357-58910370 chr11:58912178-58912199 chr11:58910357-58910369 chr11:58910356-58910376 chr11:58910358-58910375
42	BCL3	chr11:58910482-58911024	A549	lung:	n/a	chr11:58910712-58910721
43	RFX5	chr11:58909364-58911041	SK-N-SH	brain:	n/a	chr11:58910569-58910578
44	POLR2A	chr11:58909809-58910975	GM12892	blood:	n/a	n/a
45	RUNX3	chr11:58909849-58911010	GM12878	blood:	n/a	n/a
46	EBF1	chr11:58910509-58910929	GM12878	blood:	n/a	n/a
47	MXI1	chr11:58909356-58910947	IMR90	lung:	n/a	n/a
48	PML	chr11:58909692-58911244	GM12878	blood:	n/a	n/a
49	E2F4	chr11:58909879-58911341	MCF10A-Er-Src	breast:	n/a	chr11:58910568-58910577 chr11:58910504-58910513
50	ATF2	chr11:58909854-58910933	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58904183..58908174-chr11:58910132..58913359,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM111B-1	chr11:58910556-58911020	NONHSAT021512

Variant related genes	Relation type
FAM111A	TF binding region
ENSG00000245571	TF binding region
ENSG00000255381	TF binding region
ENSG00000245571	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10128605	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10128661	0.86[EUR][1000 genomes]
rs10437720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10792219	0.95[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs10792221	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896914	0.87[EUR][1000 genomes]
rs10896922	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10896924	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs10896925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896926	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896929	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896931	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896932	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896933	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10896934	0.84[EUR][1000 genomes]
rs10896935	0.82[EUR][1000 genomes]
rs10896936	0.90[EUR][1000 genomes]
rs10896937	0.90[EUR][1000 genomes]
rs10896938	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896947	0.89[CEU][hapmap]
rs11229798	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs11229799	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs11229800	0.94[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs11229801	0.90[EUR][1000 genomes]
rs11229837	0.95[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229851	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229852	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229854	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229856	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11823977	0.93[EUR][1000 genomes]
rs11825017	0.93[EUR][1000 genomes]
rs12271831	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12272113	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12274008	0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12275487	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12278163	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12280068	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12283633	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12292185	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12293649	0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12293695	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12362905	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12802129	0.93[EUR][1000 genomes]
rs17153379	0.93[EUR][1000 genomes]
rs17153383	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17153415	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1938588	0.93[EUR][1000 genomes]
rs1938589	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938781	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096544	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2096586	0.86[EUR][1000 genomes]
rs2096587	0.89[EUR][1000 genomes]
rs2105506	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2105507	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2154628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186380	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2282482	0.91[EUR][1000 genomes]
rs2282483	0.90[EUR][1000 genomes]
rs2839968	0.89[CEU][hapmap]
rs2849739	0.85[EUR][1000 genomes]
rs34027305	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34239454	0.89[EUR][1000 genomes]
rs34501069	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35293773	0.89[EUR][1000 genomes]
rs3802961	0.93[EUR][1000 genomes]
rs474847	0.88[EUR][1000 genomes]
rs55657403	0.85[EUR][1000 genomes]
rs55689653	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55989038	0.84[EUR][1000 genomes]
rs56137001	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56239606	0.84[EUR][1000 genomes]
rs58722008	0.87[EUR][1000 genomes]
rs61902181	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61902223	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7126078	0.93[EUR][1000 genomes]
rs7933787	1.00[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];0.95[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7950880	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11229840	OR5AK2	cis	parietal	SCAN
rs11229840	C11orf31	cis	parietal	SCAN
rs11229840	FAM111A	cis	parietal	SCAN
rs11229840	CD5	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58908800-58913600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:58909000-58911400	Active TSS	GM12878-XiMat	blood
3	chr11:58909200-58911000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:58909200-58911000	Active TSS	HMEC	breast
5	chr11:58909400-58911000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:58909400-58911000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:58909400-58911000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr11:58909400-58911000	Active TSS	Osteobl	bone
9	chr11:58909400-58911200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr11:58909400-58911200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr11:58909400-58911200	Active TSS	Muscle Satellite Cultured Cells	--
12	chr11:58909400-58911200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr11:58909400-58911200	Active TSS	NHLF	lung
14	chr11:58909400-58911400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr11:58909400-58911400	Active TSS	Fetal Intestine Large	intestine
16	chr11:58909400-58911400	Active TSS	Fetal Intestine Small	intestine
17	chr11:58909400-58911400	Active TSS	Fetal Stomach	stomach
18	chr11:58909400-58912000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:58909400-58912200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:58909400-58913200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr11:58909400-58913400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:58909400-58913400	Active TSS	NHDF-Ad	bronchial
23	chr11:58909400-58914000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr11:58909600-58911000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:58909600-58911000	Active TSS	Brain Cingulate Gyrus	brain
26	chr11:58909600-58911000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:58909600-58911000	Active TSS	Brain Substantia Nigra	brain
28	chr11:58909600-58911000	Active TSS	Colonic Mucosa	Colon
29	chr11:58909600-58911000	Active TSS	Colon Smooth Muscle	Colon
30	chr11:58909600-58911000	Active TSS	Pancreas	Pancrea
31	chr11:58909600-58911200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr11:58909600-58911200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr11:58909600-58911200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:58909600-58911200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:58909600-58911200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:58909600-58912000	Active TSS	Brain Germinal Matrix	brain
37	chr11:58909600-58912200	Active TSS	Psoas Muscle	Psoas
38	chr11:58909600-58912200	Active TSS	Right Atrium	heart
39	chr11:58909600-58912200	Active TSS	Right Ventricle	heart
40	chr11:58909600-58912600	Active TSS	Aorta	Aorta
41	chr11:58909600-58912600	Active TSS	HSMMtube	muscle
42	chr11:58909800-58911000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr11:58909800-58911000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:58909800-58911000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr11:58909800-58911000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:58909800-58911000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:58909800-58911000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr11:58909800-58911000	Active TSS	Brain Hippocampus Middle	brain
49	chr11:58909800-58911000	Active TSS	Esophagus	oesophagus
50	chr11:58909800-58911000	Active TSS	Gastric	stomach

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