Variant report

Variant	rs733590
Chromosome Location	chr6:36645203-36645204
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	STAT3	chr6:36645054-36646335	MCF10A-Er-Src	breast:	n/a	chr6:36645802-36645822 chr6:36645808-36645817 chr6:36645808-36645816 chr6:36645802-36645822 chr6:36645807-36645816
2	RUNX3	chr6:36644763-36645901	GM12878	blood:	n/a	n/a
3	KAP1	chr6:36644788-36646792	HEK293	kidney:	n/a	n/a
4	NFIC	chr6:36645088-36646823	HepG2	liver:	n/a	n/a
5	HEY1	chr6:36644699-36647538	HepG2	liver:	n/a	chr6:36646439-36646454 chr6:36646399-36646414
6	RAD21	chr6:36643874-36649108	SK-N-SH	brain:	n/a	chr6:36644187-36644201 chr6:36646425-36646439 chr6:36646938-36646951 chr6:36647756-36647766 chr6:36644031-36644045
7	POLR2A	chr6:36644720-36645332	GM12892	blood:	n/a	n/a
8	ZEB1	chr6:36644713-36647578	HepG2	liver:	n/a	n/a
9	CTCF	chr6:36644682-36649046	SK-N-SH	brain:	n/a	chr6:36644843-36644861 chr6:36647784-36647797 chr6:36646423-36646441 chr6:36645963-36645970 chr6:36647827-36647836 chr6:36647770-36647780
10	POLR2A	chr6:36644755-36645214	HepG2	liver:	n/a	n/a
11	MXI1	chr6:36643959-36649033	IMR90	lung:	n/a	n/a
12	POLR2A	chr6:36643939-36647410	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:36644766-36648199	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr6:36644776-36645864	GM19193	blood:	n/a	n/a
15	PML	chr6:36644718-36649008	GM12878	blood:	n/a	chr6:36648003-36648012
16	POLR2A	chr6:36644702-36645953	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:36644846-36645354	GM12878	blood:	n/a	n/a
18	MAX	chr6:36643823-36648608	HepG2	liver:	n/a	chr6:36648002-36648011
19	POLR2A	chr6:36644830-36649007	GM12878	blood:	n/a	n/a
20	RELA	chr6:36645060-36646770	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:36644736-36646047	HepG2	liver:	n/a	n/a
22	MXI1	chr6:36643752-36648956	SK-N-SH	brain:	n/a	n/a
23	TAF1	chr6:36644951-36645216	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr6:36644081-36649028	IMR90	lung:	n/a	n/a
25	POLR2A	chr6:36644870-36645864	HepG2	liver:	n/a	n/a
26	MYBL2	chr6:36644928-36647408	HepG2	liver:	n/a	n/a
27	NFIC	chr6:36645074-36647075	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:36644855-36645258	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr6:36644752-36645245	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:36644651-36645314	GM12891	blood:	n/a	n/a
31	NFIC	chr6:36644925-36646697	HepG2	liver:	n/a	n/a
32	MYBL2	chr6:36643933-36646660	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:36643627-36647609	HepG2	liver:	n/a	n/a
34	STAT5A	chr6:36644796-36645214	GM12878	blood:	n/a	n/a
35	HEY1	chr6:36644712-36645339	HepG2	liver:	n/a	n/a
36	REST	chr6:36644931-36645350	MCF-7	breast:	n/a	n/a
37	POLR2A	chr6:36643787-36657761	GM12891	blood:	n/a	n/a
38	IKZF1	chr6:36644976-36646231	GM12878	blood:	n/a	chr6:36645950-36645958
39	KAP1	chr6:36644053-36645893	U2OS	brain:	n/a	n/a
40	POLR2A	chr6:36644775-36645312	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:36643814-36656801	GM12878	blood:	n/a	n/a
42	MBD4	chr6:36643803-36647135	HepG2	liver:	n/a	n/a
43	MAX	chr6:36643809-36647379	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:36644718-36649084	GM12891	blood:	n/a	n/a
45	POLR2A	chr6:36644815-36649061	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:36645053-36645267	GM12891	blood:	n/a	n/a
47	ZNF143	chr6:36644879-36645204	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:36644968-36645329	MCF10A-Er-Src	breast:	n/a	n/a
49	CHD1	chr6:36644991-36645876	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:36643719-36649046	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
2	chr6:36644040..36648031-chr6:36680924..36685784,5	MCF-7	breast:
3	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
4	chr6:36559895..36571260-chr6:36642384..36648914,19	MCF-7	breast:
5	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
6	chr6:36581748..36603537-chr6:36641861..36652365,77	MCF-7	breast:

Variant related genes	Relation type
CDKN1A	TF binding region
ENSG00000112081	Chromatin interaction
ENSG00000263894	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000255587	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10807170	0.93[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2395655	0.84[CEU][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3176320	0.88[CEU][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3176323	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3176334	0.84[CEU][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4135240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4711456	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711457	0.93[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs4713996	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713999	0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs4714001	0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930083	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs9394368	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs733590	PI16	cis	parietal	SCAN
rs733590	SPDEF	cis	cerebellum	SCAN
rs733590	GRM4	cis	cerebellum	SCAN
rs733590	CDKN1A	cis	multi-tissue	Pritchard
rs733590	SNRPC	cis	cerebellum	SCAN
rs733590	LHFPL5	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
2	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:36642400-36646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:36643600-36646000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr6:36643800-36645400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:36643800-36645400	Enhancers	NHDF-Ad	bronchial
7	chr6:36643800-36645600	Enhancers	Adipose Nuclei	Adipose
8	chr6:36643800-36645600	Enhancers	Brain Angular Gyrus	brain
9	chr6:36643800-36645600	Enhancers	Fetal Intestine Large	intestine
10	chr6:36643800-36645600	Enhancers	Fetal Intestine Small	intestine
11	chr6:36643800-36645600	Enhancers	A549	lung
12	chr6:36643800-36645600	Enhancers	NHLF	lung
13	chr6:36643800-36645600	Enhancers	Osteobl	bone
14	chr6:36643800-36645800	Enhancers	HUVEC	blood vessel
15	chr6:36643800-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:36643800-36646000	Enhancers	Brain Substantia Nigra	brain
17	chr6:36643800-36646000	Enhancers	NH-A	brain
18	chr6:36643800-36646200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:36643800-36646200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:36643800-36646400	Bivalent Enhancer	Fetal Thymus	thymus
21	chr6:36643800-36646400	Enhancers	Pancreas	Pancrea
22	chr6:36643800-36646400	Enhancers	Stomach Mucosa	stomach
23	chr6:36643800-36646400	Flanking Active TSS	NHEK	skin
24	chr6:36644000-36645400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:36644000-36645400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr6:36644000-36645400	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr6:36644000-36645600	Enhancers	Duodenum Mucosa	Duodenum
28	chr6:36644000-36645600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:36644000-36645600	Enhancers	Hela-S3	cervix
30	chr6:36644000-36646000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:36644000-36646000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:36644000-36646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:36644000-36646000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:36644000-36646000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:36644000-36646000	Enhancers	Brain Anterior Caudate	brain
36	chr6:36644000-36646000	Enhancers	Colonic Mucosa	Colon
37	chr6:36644000-36646000	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr6:36644000-36646200	Enhancers	Esophagus	oesophagus
39	chr6:36644000-36646200	Flanking Active TSS	HSMM	muscle
40	chr6:36644000-36646400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:36644000-36646400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:36644000-36646400	Enhancers	Placenta	Placenta
43	chr6:36644000-36646400	Enhancers	Lung	lung
44	chr6:36644000-36646400	Flanking Active TSS	HMEC	breast
45	chr6:36644200-36645600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr6:36644200-36645600	Flanking Bivalent TSS/Enh	HepG2	liver
47	chr6:36644200-36646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:36644200-36646200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:36644200-36647600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:36644400-36645400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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