Variant report

Variant	rs3763869
Chromosome Location	chr11:9594827-9594828
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	TAF1	chr11:9594342-9595651	HepG2	liver:	n/a	n/a
2	JUND	chr11:9594585-9595242	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:9594236-9595686	PFSK-1	brain:	n/a	n/a
4	UBTF	chr11:9594411-9597195	K562	blood:	n/a	n/a
5	FOXA1	chr11:9594088-9595260	HepG2	liver:	n/a	n/a
6	REST	chr11:9594492-9595401	H1-neurons	neurons:	n/a	chr11:9594524-9594542
7	POLR2A	chr11:9594325-9595577	HUVEC	blood vessel:	n/a	n/a
8	MYC	chr11:9594410-9595561	K562	blood:	n/a	chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9595391-9595400 chr11:9595188-9595197 chr11:9595392-9595399
9	TAF1	chr11:9594283-9595978	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr11:9594224-9596603	GM12878	blood:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
11	PML	chr11:9594694-9595010	GM12878	blood:	n/a	n/a
12	E2F6	chr11:9594352-9595659	Hela-S3	cervix:	n/a	chr11:9595087-9595097 chr11:9595083-9595094 chr11:9595086-9595097 chr11:9595089-9595096 chr11:9595344-9595354 chr11:9595363-9595373 chr11:9595088-9595096 chr11:9595088-9595096 chr11:9595085-9595096 chr11:9595292-9595301 chr11:9595088-9595096 chr11:9595201-9595213
13	MAX	chr11:9594250-9595554	K562	blood:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
14	MAX	chr11:9594248-9595832	K562	blood:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
15	STAT1	chr11:9594689-9595540	GM12878	blood:	n/a	n/a
16	TAF7	chr11:9594545-9597218	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYBL2	chr11:9594191-9595591	HepG2	liver:	n/a	n/a
18	NFIC	chr11:9594471-9595411	GM12878	blood:	n/a	n/a
19	ELF1	chr11:9594392-9595660	K562	blood:	n/a	chr11:9595271-9595283 chr11:9595060-9595072 chr11:9595346-9595355 chr11:9594821-9594830 chr11:9595301-9595310
20	POLR2A	chr11:9594277-9595726	GM12892	blood:	n/a	n/a
21	ZNF384	chr11:9594555-9595346	GM12878	blood:	n/a	n/a
22	MXI1	chr11:9593222-9598393	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr11:9594208-9595540	U87	brain:	n/a	n/a
24	RFX5	chr11:9594414-9595535	Hela-S3	cervix:	n/a	n/a
25	MAX	chr11:9594223-9595573	HUVEC	blood vessel:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
26	CEBPD	chr11:9594688-9595164	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:9594287-9597716	PBDE	blood:	n/a	n/a
28	HNF4G	chr11:9594509-9595270	HepG2	liver:	n/a	chr11:9594771-9594793
29	NFIC	chr11:9594172-9595518	ECC-1	luminal epithelium:	n/a	n/a
30	TCF12	chr11:9594330-9595029	GM12878	blood:	n/a	n/a
31	POLR2A	chr11:9594400-9594978	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:9593829-9601404	MCF10A-Er-Src	breast:	n/a	n/a
33	NFIC	chr11:9594166-9595416	ECC-1	luminal epithelium:	n/a	n/a
34	E2F6	chr11:9594200-9595394	A549	lung:	n/a	chr11:9595087-9595097 chr11:9595083-9595094 chr11:9595086-9595097 chr11:9595089-9595096 chr11:9595344-9595354 chr11:9595363-9595373 chr11:9595088-9595096 chr11:9595088-9595096 chr11:9595085-9595096 chr11:9595292-9595301 chr11:9595088-9595096 chr11:9595201-9595213
35	YY1	chr11:9594287-9594885	SK-N-SH	brain:	n/a	chr11:9594821-9594835 chr11:9594838-9594849 chr11:9594831-9594842
36	ZBTB7A	chr11:9594412-9595120	ECC-1	luminal epithelium:	n/a	n/a
37	ELF1	chr11:9594317-9595394	K562	blood:	n/a	chr11:9595271-9595283 chr11:9595060-9595072 chr11:9595346-9595355 chr11:9594821-9594830 chr11:9595301-9595310
38	HEY1	chr11:9594201-9595598	HepG2	liver:	n/a	chr11:9595294-9595309 chr11:9595297-9595312 chr11:9595341-9595356 chr11:9594830-9594845
39	BCLAF1	chr11:9594757-9595642	K562	blood:	n/a	chr11:9595432-9595445 chr11:9595295-9595308 chr11:9595294-9595303 chr11:9595332-9595345 chr11:9594834-9594847 chr11:9595345-9595354 chr11:9595343-9595356
40	SIN3AK20	chr11:9594290-9594960	HepG2	liver:	n/a	n/a
41	SIN3A	chr11:9594255-9595851	GM12878	blood:	n/a	chr11:9595382-9595393 chr11:9594766-9594779
42	ZKSCAN1	chr11:9594364-9595554	Hela-S3	cervix:	n/a	n/a
43	EP300	chr11:9594513-9595392	K562	blood:	n/a	chr11:9595325-9595341 chr11:9595338-9595354 chr11:9595351-9595367 chr11:9594759-9594775 chr11:9595344-9595353
44	NR2F2	chr11:9594512-9595328	K562	blood:	n/a	n/a
45	NR2F2	chr11:9594123-9595362	K562	blood:	n/a	n/a
46	E2F4	chr11:9594768-9595380	MCF10A-Er-Src	breast:	n/a	chr11:9595087-9595097 chr11:9595086-9595097 chr11:9595089-9595096 chr11:9595344-9595354 chr11:9595363-9595373 chr11:9595088-9595096 chr11:9595088-9595096 chr11:9595085-9595096 chr11:9595292-9595301 chr11:9595088-9595096 chr11:9595201-9595213 chr11:9595083-9595094
47	RAD21	chr11:9594391-9595780	IMR90	lung:	n/a	chr11:9594697-9594709 chr11:9595405-9595415 chr11:9595340-9595353 chr11:9595386-9595400
48	MAX	chr11:9594214-9595556	HepG2	liver:	n/a	chr11:9594393-9594404 chr11:9594393-9594403 chr11:9595186-9595197 chr11:9595186-9595197 chr11:9595391-9595400 chr11:9594394-9594403 chr11:9595391-9595400 chr11:9594395-9594402 chr11:9594390-9594405 chr11:9595188-9595197 chr11:9594392-9594407 chr11:9595392-9595399
49	JUND	chr11:9594333-9595379	K562	blood:	n/a	chr11:9595268-9595277
50	POLR2A	chr11:9594122-9595677	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9594432..9594977-chr20:30194249..30195144,2	Hela-S3	cervix:
2	chr11:9112943..9114701-chr11:9593377..9596594,3	MCF-7	breast:
3	chr11:9594244..9596039-chr11:9777459..9779743,2	MCF-7	breast:
4	chr11:9479099..9485582-chr11:9593306..9599058,18	K562	blood:
5	chr11:9482166..9483015-chr11:9594207..9594915,2	Hela-S3	cervix:
6	chr1:234744714..234746851-chr11:9594601..9596102,2	MCF-7	breast:
7	chr11:8702253..8704416-chr11:9593339..9594880,2	MCF-7	breast:
8	chr11:9593380..9601954-chr11:9626466..9639393,32	K562	blood:
9	chr11:9478618..9485582-chr11:9593299..9599536,13	K562	blood:
10	chr11:9594508..9596451-chr11:10325420..10327263,2	MCF-7	breast:
11	chr11:9594404..9594909-chr19:56632177..56632899,2	Hela-S3	cervix:
12	chr11:9480226..9484903-chr11:9591788..9598525,12	MCF-7	breast:
13	chr11:9594464..9595108-chr22:30591798..30592673,2	Hela-S3	cervix:
14	chr11:9594577..9595173-chr3:114865177..114865799,2	Hela-S3	cervix:
15	chr11:9593146..9594870-chr11:9635191..9636726,2	MCF-7	breast:

Variant related genes	Relation type
WEE1	TF binding region
ENSG00000238387	TF binding region
ENSG00000166441	Chromatin interaction
ENSG00000168264	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000245522	Chromatin interaction
ENSG00000148926	Chromatin interaction
ENSG00000175356	Chromatin interaction
ENSG00000243964	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10840269	0.81[CHB][hapmap]
rs3763868	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3870635	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3910384	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.83[ASN][1000 genomes]
rs4370932	0.92[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs6486433	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv3365334	chr11:9593876-9597474	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
4	esv3439005	chr11:9593901-9596949	Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3395275	chr11:9594426-9597274	Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	n/a
6	esv3330950	chr11:9594801-9597349	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3763869	PTH	cis	cerebellum	SCAN
rs3763869	OR56A4	cis	parietal	SCAN
rs3763869	SWAP70	cis	lymphoblastoid	seeQTL
rs3763869	SWAP70	Cis_1M	lymphoblastoid	RTeQTL
rs3763869	SNORA23	cis	parietal	SCAN
rs3763869	MICAL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9591600-9596200	Weak transcription	Fetal Heart	heart
2	chr11:9593600-9595800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:9593600-9596200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr11:9593600-9596600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr11:9593600-9598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:9593800-9596400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:9593800-9596400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:9593800-9596400	Active TSS	HepG2	liver
9	chr11:9593800-9596400	Active TSS	Osteobl	bone
10	chr11:9593800-9596600	Active TSS	Brain Hippocampus Middle	brain
11	chr11:9593800-9597200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr11:9593800-9597400	Active TSS	A549	lung
13	chr11:9593800-9597800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr11:9593800-9598200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr11:9593800-9599000	Active TSS	Psoas Muscle	Psoas
16	chr11:9593800-9599600	Active TSS	Brain Germinal Matrix	brain
17	chr11:9593800-9599800	Active TSS	HSMMtube	muscle
18	chr11:9594000-9595000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:9594000-9595000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:9594000-9596200	Active TSS	Adipose Nuclei	Adipose
21	chr11:9594000-9596400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:9594000-9596400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:9594000-9596400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr11:9594000-9597200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:9594000-9597200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr11:9594000-9597800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:9594000-9597800	Active TSS	Duodenum Mucosa	Duodenum
28	chr11:9594000-9598000	Active TSS	NHEK	skin
29	chr11:9594000-9598200	Active TSS	HSMM	muscle
30	chr11:9594000-9598600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr11:9594000-9598800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:9594000-9599400	Active TSS	Fetal Brain Female	brain
33	chr11:9594200-9595000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr11:9594200-9595400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:9594200-9596400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:9594200-9596400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr11:9594200-9596400	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr11:9594200-9596600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:9594200-9596600	Active TSS	Brain Angular Gyrus	brain
40	chr11:9594200-9596600	Active TSS	Brain Cingulate Gyrus	brain
41	chr11:9594200-9596600	Active TSS	Brain Substantia Nigra	brain
42	chr11:9594200-9596600	Active TSS	Fetal Lung	lung
43	chr11:9594200-9596600	Active TSS	Rectal Smooth Muscle	rectum
44	chr11:9594200-9597000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:9594200-9597200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr11:9594200-9597600	Active TSS	Brain Anterior Caudate	brain
47	chr11:9594200-9597600	Active TSS	Colonic Mucosa	Colon
48	chr11:9594200-9597800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:9594200-9598000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:9594200-9598000	Active TSS	Rectal Mucosa Donor 29	rectum

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