Variant report

Variant	rs11229841
Chromosome Location	chr11:58912147-58912148
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	chr11:58911912-58912607	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:58912025-58912618	K562	blood:	n/a	n/a
3	CUX1	chr11:58912053-58912382	K562	blood:	n/a	n/a
4	BHLHE40	chr11:58911978-58912514	GM12878	blood:	n/a	n/a
5	MXI1	chr11:58911027-58913404	IMR90	lung:	n/a	n/a
6	NFYA	chr11:58912049-58912448	GM12878	blood:	n/a	n/a
7	RFX5	chr11:58912105-58912368	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:58911418-58912899	GM12878	blood:	n/a	n/a
9	STAT3	chr11:58911974-58912406	MCF10A-Er-Src	breast:	n/a	chr11:58912223-58912234
10	RCOR1	chr11:58911957-58912932	K562	blood:	n/a	n/a
11	MAX	chr11:58911719-58912886	A549	lung:	n/a	chr11:58911800-58911809
12	SP1	chr11:58911803-58912582	A549	lung:	n/a	chr11:58912561-58912575
13	POLR2A	chr11:58911921-58912708	PANC-1	pancreas:	n/a	n/a
14	ELK1	chr11:58912078-58912556	Hela-S3	cervix:	n/a	n/a
15	TBL1XR1	chr11:58912064-58912532	GM12878	blood:	n/a	n/a
16	MAX	chr11:58911729-58912890	HCT-116	colon:	n/a	chr11:58911800-58911809
17	MAX	chr11:58911846-58912860	H1-hESC	embryonic stem cell:	n/a	n/a
18	MXI1	chr11:58912015-58912440	K562	blood:	n/a	n/a
19	CBX3	chr11:58911865-58912631	K562	blood:	n/a	n/a
20	POLR2A	chr11:58912020-58912684	Gliobla	brain:	n/a	n/a
21	POU2F2	chr11:58911999-58912443	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:58909722-58913181	GM12891	blood:	n/a	n/a
23	POLR2A	chr11:58911622-58913239	Hela-S3	cervix:	n/a	n/a
24	GABPA	chr11:58911959-58912514	MCF-7	breast:	n/a	n/a
25	RFX5	chr11:58912006-58912368	GM12878	blood:	n/a	n/a
26	ZNF143	chr11:58912135-58912870	H1-hESC	embryonic stem cell:	n/a	chr11:58912565-58912583 chr11:58912378-58912396 chr11:58912442-58912460
27	EP300	chr11:58911994-58912495	A549	lung:	n/a	n/a
28	STAT3	chr11:58912061-58912392	MCF10A-Er-Src	breast:	n/a	chr11:58912223-58912234
29	MAZ	chr11:58912038-58912662	GM12878	blood:	n/a	n/a
30	ETS1	chr11:58911919-58912505	A549	lung:	n/a	n/a
31	ZNF143	chr11:58912129-58912554	K562	blood:	n/a	chr11:58912378-58912396 chr11:58912442-58912460
32	POLR2A	chr11:58911910-58912577	GM12892	blood:	n/a	n/a
33	ELK1	chr11:58911925-58912435	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:58912143-58912647	MCF-7	breast:	n/a	n/a
35	NFYA	chr11:58912052-58912474	K562	blood:	n/a	n/a
36	MAX	chr11:58911945-58912845	H1-hESC	embryonic stem cell:	n/a	n/a
37	ELF1	chr11:58912109-58912731	GM12878	blood:	n/a	n/a
38	GTF2F1	chr11:58912004-58912869	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYC	chr11:58911952-58912499	NB4	blood:	n/a	n/a
40	EP300	chr11:58912019-58912364	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:58911886-58912747	PANC-1	pancreas:	n/a	n/a
42	STAT1	chr11:58911981-58912497	GM12878	blood:	n/a	n/a
43	ATF1	chr11:58911981-58912503	K562	blood:	n/a	n/a
44	ETS1	chr11:58911982-58912447	GM12878	blood:	n/a	n/a
45	POLR2A	chr11:58911724-58912631	MCF-7	breast:	n/a	n/a
46	POLR2A	chr11:58911942-58912720	K562	blood:	n/a	n/a
47	STAT3	chr11:58912042-58912436	MCF10A-Er-Src	breast:	n/a	chr11:58912223-58912234
48	ATF2	chr11:58911894-58912591	GM12878	blood:	n/a	n/a
49	TBP	chr11:58911968-58912618	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr11:58911373-58912958	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58911158..58913877-chr11:58937423..58939058,2	K562	blood:
2	chr11:58904183..58908174-chr11:58910132..58913359,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245571	TF binding region
ENSG00000255381	TF binding region
FAM111A	TF binding region
ENSG00000245571	Chromatin interaction
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048374	1.00[EUR][1000 genomes]
rs10896948	1.00[CEU][hapmap]
rs10896954	1.00[CEU][hapmap]
rs11229810	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs11229821	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229829	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229831	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229832	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229838	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229842	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229844	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11229858	0.91[ASN][1000 genomes]
rs11229862	0.81[ASN][1000 genomes]
rs11229871	1.00[CEU][hapmap]
rs11229891	1.00[CEU][hapmap]
rs11229905	1.00[CEU][hapmap]
rs12221768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12222675	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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12223473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs12225532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12275736	1.00[CEU][hapmap]
rs17153381	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2154626	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2154627	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2154964	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2154965	1.00[EUR][1000 genomes]
rs35732637	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55742277	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56349021	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57969871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58277547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60519524	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60795438	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60883299	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951382	1.00[CEU][hapmap]

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

No data

Chromatin state (count:123 , 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	chr11:58909400-58912200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:58909400-58913200	Active TSS	H1 Cell Line	embryonic stem cell
4	chr11:58909400-58913400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:58909400-58913400	Active TSS	NHDF-Ad	bronchial
6	chr11:58909400-58914000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr11:58909600-58912200	Active TSS	Psoas Muscle	Psoas
8	chr11:58909600-58912200	Active TSS	Right Atrium	heart
9	chr11:58909600-58912200	Active TSS	Right Ventricle	heart
10	chr11:58909600-58912600	Active TSS	Aorta	Aorta
11	chr11:58909600-58912600	Active TSS	HSMMtube	muscle
12	chr11:58909800-58912200	Active TSS	Left Ventricle	heart
13	chr11:58909800-58912400	Active TSS	Rectal Smooth Muscle	rectum
14	chr11:58909800-58912600	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr11:58910000-58912400	Active TSS	Fetal Brain Female	brain
16	chr11:58910600-58912200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr11:58910600-58913000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr11:58910600-58913000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr11:58910600-58913200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr11:58910600-58913400	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr11:58910600-58913400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:58910600-58913400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:58910600-58913400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:58910800-58912200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:58910800-58912200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:58910800-58912200	Flanking Active TSS	Hela-S3	cervix
27	chr11:58910800-58912800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr11:58910800-58913000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr11:58910800-58913400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:58910800-58913600	Flanking Active TSS	HUVEC	blood vessel
31	chr11:58910800-58914200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr11:58911000-58912200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:58911000-58912200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr11:58911000-58912200	Active TSS	Fetal Muscle Trunk	muscle
35	chr11:58911000-58912200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr11:58911000-58912200	Flanking Active TSS	Dnd41	blood
37	chr11:58911000-58912200	Flanking Active TSS	K562	blood
38	chr11:58911000-58912200	Flanking Active TSS	NHEK	skin
39	chr11:58911000-58912200	Flanking Active TSS	Osteobl	bone
40	chr11:58911000-58912400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr11:58911000-58912800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr11:58911000-58912800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr11:58911000-58913600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:58911200-58912200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:58911200-58912200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:58911200-58912400	Active TSS	Brain Angular Gyrus	brain
47	chr11:58911200-58912600	Active TSS	Thymus	Thymus
48	chr11:58911200-58913800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr11:58911400-58912200	Flanking Active TSS	HMEC	breast
50	chr11:58911400-58913000	Flanking Active TSS	Fetal Stomach	stomach

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