Variant report

Variant	rs7130020
Chromosome Location	chr11:57079471-57079472
allele	A/G
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	chr11:57075726-57080675	PFSK-1	brain:	n/a	n/a
2	RCOR1	chr11:57079302-57079644	K562	blood:	n/a	n/a
3	POLR2A	chr11:57078440-57079614	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr11:57078292-57079534	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF143	chr11:57079380-57079573	K562	blood:	n/a	n/a
6	POLR2A	chr11:57078028-57079498	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr11:57076375-57080927	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr11:57079202-57079582	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:57077940-57080942	K562	blood:	n/a	n/a
10	MAZ	chr11:57077810-57079849	IMR90	lung:	n/a	n/a
11	RCOR1	chr11:57078116-57079511	Hela-S3	cervix:	n/a	n/a
12	TCF12	chr11:57078305-57079518	SK-N-SH	brain:	n/a	chr11:57079185-57079195 chr11:57078862-57078872 chr11:57079130-57079140
13	POLR2A	chr11:57075814-57080948	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:57077655-57079547	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:57075206-57079517	U87	brain:	n/a	n/a
16	USF2	chr11:57079346-57080175	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr11:57077177-57079542	IMR90	lung:	n/a	chr11:57079185-57079194
18	POLR2A	chr11:57075206-57079814	U87	brain:	n/a	n/a
19	POLR2A	chr11:57079454-57080878	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:57078030-57079700	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr11:57079241-57079506	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAZ	chr11:57078536-57079495	K562	blood:	n/a	n/a
23	FOSL2	chr11:57078178-57079473	A549	lung:	n/a	chr11:57079015-57079025 chr11:57079090-57079099 chr11:57078701-57078713 chr11:57078704-57078715 chr11:57078702-57078713 chr11:57078703-57078711 chr11:57079016-57079024
24	NFIC	chr11:57078052-57079697	ECC-1	luminal epithelium:	n/a	chr11:57078348-57078365 chr11:57078348-57078364 chr11:57078350-57078366
25	POLR2A	chr11:57078207-57079582	IMR90	lung:	n/a	n/a
26	POLR2A	chr11:57079223-57079604	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:57078050-57079598	H1-hESC	embryonic stem cell:	n/a	n/a
28	JUN	chr11:57077965-57079989	K562	blood:	n/a	chr11:57079015-57079025 chr11:57079090-57079099 chr11:57078701-57078713 chr11:57078704-57078715 chr11:57078702-57078713 chr11:57078703-57078711 chr11:57079016-57079024
29	POLR2A	chr11:57078011-57079590	Hela-S3	cervix:	n/a	n/a
30	FOSL1	chr11:57078391-57079475	HCT-116	colon:	n/a	chr11:57079015-57079025 chr11:57079090-57079099 chr11:57078701-57078713 chr11:57078704-57078715 chr11:57078702-57078713 chr11:57078703-57078711 chr11:57079016-57079024
31	NFIC	chr11:57078029-57079503	ECC-1	luminal epithelium:	n/a	chr11:57078348-57078365 chr11:57078348-57078364 chr11:57078350-57078366
32	STAT3	chr11:57079119-57079482	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
TNKS1BP1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10732882	0.93[CHD][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs10792083	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10792085	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10896596	0.91[ASN][1000 genomes]
rs10896601	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896602	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10896609	0.80[ASN][1000 genomes]
rs11228971	0.91[ASN][1000 genomes]
rs11228988	0.88[ASN][1000 genomes]
rs11602501	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604373	0.88[ASN][1000 genomes]
rs17573746	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1939496	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276042	0.82[CHD][hapmap]
rs3935069	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939129	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939131	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4939134	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5012051	0.85[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs55637147	0.82[ASN][1000 genomes]
rs7928905	0.88[ASN][1000 genomes]
rs7931298	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7936545	0.85[ASN][1000 genomes]
rs7943761	0.88[ASN][1000 genomes]
rs7943915	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7948723	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs879646	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv541048	chr11:57076815-57120781	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7130020	GLYATL2	cis	parietal	SCAN
rs7130020	OR4C6	cis	parietal	SCAN
rs7130020	OR9I1	cis	cerebellum	SCAN
rs7130020	PRPF19	cis	cerebellum	SCAN
rs7130020	OR5M9	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57068400-57081600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57074400-57081800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:57075000-57080600	Genic enhancers	Spleen	Spleen
4	chr11:57076200-57080600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:57077600-57082200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:57077800-57079600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:57077800-57080000	Genic enhancers	Brain Substantia Nigra	brain
8	chr11:57077800-57080000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
9	chr11:57078000-57079600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:57078000-57079800	Enhancers	Fetal Heart	heart
11	chr11:57078000-57080000	Genic enhancers	Brain Cingulate Gyrus	brain
12	chr11:57078000-57080600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr11:57078200-57079600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:57078200-57079600	Flanking Active TSS	Colonic Mucosa	Colon
15	chr11:57078200-57079600	Enhancers	Fetal Brain Male	brain
16	chr11:57078200-57079600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr11:57078400-57079600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr11:57078400-57079600	Enhancers	Primary B cells from peripheral blood	blood
19	chr11:57078400-57079600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:57078400-57079600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:57078400-57079600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr11:57078400-57079600	Flanking Active TSS	Fetal Muscle Trunk	muscle
23	chr11:57078400-57079800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:57078600-57079600	Enhancers	Primary T cells from cord blood	blood
25	chr11:57078600-57079600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:57078600-57079600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr11:57079000-57079600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:57079000-57079600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:57079000-57079600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:57079000-57079600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr11:57079000-57079800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr11:57079000-57079800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr11:57079000-57079800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:57079000-57079800	Enhancers	Primary hematopoietic stem cells	blood
35	chr11:57079000-57079800	Weak transcription	Aorta	Aorta
36	chr11:57079000-57079800	Enhancers	Pancreas	Pancrea
37	chr11:57079000-57080000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:57079000-57080000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr11:57079000-57080000	Enhancers	Lung	lung
40	chr11:57079000-57080000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr11:57079000-57080600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:57079000-57080800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:57079000-57081400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr11:57079000-57081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:57079200-57079600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:57079200-57079600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:57079200-57079600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr11:57079200-57079600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr11:57079200-57079600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:57079200-57079600	Flanking Active TSS	Adipose Nuclei	Adipose

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