Variant report

Variant	rs8113682
Chromosome Location	chr19:19743730-19743731
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19743422-19743835	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:19743395-19743977	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:19743365-19743839	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:19743347-19743826	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:19743296-19743880	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:19743364-19743953	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:19743541-19743756	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:19743355-19743926	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:19743448-19743839	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:19743281-19744234	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:19743362-19743839	GM12892	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19702415..19703999-chr19:19742408..19743931,2	MCF-7	breast:
2	chr19:19650704..19652746-chr19:19743120..19746086,2	K562	blood:
3	chr19:19736608..19739884-chr19:19741504..19746062,6	K562	blood:
4	chr19:19742582..19744978-chr19:19752579..19757681,5	MCF-7	breast:
5	chr19:19739295..19742489-chr19:19743481..19745918,5	MCF-7	breast:
6	chr19:19743070..19745753-chr19:20069128..20070689,2	MCF-7	breast:
7	chr19:19743338..19745792-chr19:19752799..19756349,4	K562	blood:

No data

Variant related genes	Relation type
LPAR2	TF binding region
ENSG00000160161	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10403759	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11878202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879838	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12976826	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16994684	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16996174	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1968047	0.94[ASN][1000 genomes]
rs2043293	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2304129	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34725331	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808974	0.98[ASN][1000 genomes]
rs7252228	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs739461	0.95[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8101679	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880090	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8113682	OR10H4	cis	parietal	SCAN
rs8113682	MED26	cis	parietal	SCAN
rs8113682	UNC13A	cis	cerebellum	SCAN
rs8113682	SUGP2	cis	parietal	SCAN
rs8113682	DDX49	cis	cerebellum	SCAN
rs8113682	IL12RB1	cis	parietal	SCAN
rs8113682	GATAD2A	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19729800-19744400	Weak transcription	HSMMtube	muscle
2	chr19:19735000-19753200	Weak transcription	K562	blood
3	chr19:19738600-19744200	Weak transcription	Liver	Liver
4	chr19:19738600-19753000	Weak transcription	Fetal Brain Male	brain
5	chr19:19738800-19752800	Weak transcription	Stomach Mucosa	stomach
6	chr19:19739000-19744000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:19739000-19744400	Weak transcription	NHDF-Ad	bronchial
8	chr19:19739000-19745000	Weak transcription	HSMM	muscle
9	chr19:19739600-19744400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr19:19739800-19744000	Weak transcription	Osteobl	bone
11	chr19:19739800-19744200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:19739800-19744200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:19739800-19744400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:19739800-19744600	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:19739800-19744800	Weak transcription	Esophagus	oesophagus
16	chr19:19739800-19744800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:19739800-19745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:19739800-19745200	Weak transcription	Right Ventricle	heart
19	chr19:19739800-19745600	Weak transcription	Ovary	ovary
20	chr19:19739800-19752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:19739800-19753200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:19739800-19753400	Weak transcription	Small Intestine	intestine
23	chr19:19739800-19753400	Weak transcription	HMEC	breast
24	chr19:19739800-19753600	Weak transcription	Brain Angular Gyrus	brain
25	chr19:19739800-19753600	Weak transcription	Brain Substantia Nigra	brain
26	chr19:19739800-19753600	Weak transcription	Left Ventricle	heart
27	chr19:19739800-19753600	Weak transcription	Right Atrium	heart
28	chr19:19740000-19744000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:19740000-19744200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr19:19740000-19744200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:19740000-19744200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:19740000-19744200	Weak transcription	Fetal Intestine Large	intestine
33	chr19:19740000-19744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:19740000-19744600	Weak transcription	Gastric	stomach
35	chr19:19740000-19744800	Weak transcription	Colonic Mucosa	Colon
36	chr19:19740000-19744800	Weak transcription	Pancreas	Pancrea
37	chr19:19740000-19745000	Weak transcription	Fetal Lung	lung
38	chr19:19740000-19745000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:19740000-19745000	Weak transcription	A549	lung
40	chr19:19740000-19745200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:19740000-19745200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr19:19740000-19746000	Weak transcription	NH-A	brain
43	chr19:19740000-19753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:19740000-19753400	Weak transcription	Brain Anterior Caudate	brain
45	chr19:19740000-19753600	Weak transcription	Fetal Kidney	kidney
46	chr19:19740200-19744200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:19740200-19745800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr19:19740200-19745800	Strong transcription	GM12878-XiMat	blood
49	chr19:19740200-19746000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:19740200-19747600	Strong transcription	Thymus	Thymus

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