Variant report

Variant	rs9535670
Chromosome Location	chr13:52029591-52029592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52029439-52029622	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr13:52029221-52031973	K562	blood:	n/a	n/a
3	POLR2A	chr13:52029567-52029702	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr13:52029550-52029597	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr13:52029296-52029895	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr13:52029509-52031916	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr13:52028897..52030915-chr13:52042337..52044657,2	MCF-7	breast:
2	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
3	chr13:52025794..52034237-chr13:52040132..52048046,20	K562	blood:
4	chr13:52025577..52029967-chr13:52343918..52348772,7	MCF-7	breast:
5	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
6	chr13:51980509..51983180-chr13:52028617..52030168,2	K562	blood:
7	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
8	chr13:52025709..52029684-chr13:52361886..52365561,3	MCF-7	breast:
9	chr13:52029332..52032158-chr13:52157074..52159871,2	K562	blood:
10	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
11	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDFY2-2	chr13:52027277-52030240	NONHSAT033912

No data

Variant related genes	Relation type
INTS6	TF binding region
ENSG00000206920	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000229906	Chromatin interaction
ENSG00000243900	Chromatin interaction
ENSG00000139668	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs17075688	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17194948	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17195020	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026526	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026527	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2274061	0.82[CEU][hapmap]
rs2274929	0.82[CEU][hapmap]
rs2408363	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3825524	0.82[CEU][hapmap]
rs56017742	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561634	0.80[EUR][1000 genomes]
rs73197809	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73197821	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73197824	0.91[EUR][1000 genomes]
rs73197826	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7321642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7328715	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7335122	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7335144	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7337450	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7989674	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7989850	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[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7996243	0.82[CEU][hapmap]
rs7998084	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs8001311	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9316541	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316546	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526752	0.81[CEU][hapmap]
rs9526758	0.98[ASN][1000 genomes]
rs9526759	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526761	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526768	0.91[EUR][1000 genomes]
rs9535645	0.82[CEU][hapmap]
rs9535646	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9535652	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535653	0.80[CEU][hapmap]
rs9535655	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535660	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535661	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535662	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535663	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535665	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535669	0.80[EUR][1000 genomes]
rs9535671	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535672	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535674	0.80[EUR][1000 genomes]
rs9535677	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535678	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535679	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535680	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535682	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535683	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535687	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9535688	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9535689	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535690	0.94[EUR][1000 genomes]
rs9535693	0.94[EUR][1000 genomes]
rs9535694	0.91[EUR][1000 genomes]
rs9535696	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9535697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535699	0.90[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs9563046	0.90[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9568600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9568603	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9568608	0.96[EUR][1000 genomes]
rs9568612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9591406	0.81[YRI][hapmap]
rs9596514	0.81[YRI][hapmap]
rs9634842	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535670	WDFY2	cis	parietal	SCAN
rs9535670	DDX26	cis	multi-tissue	Pritchard
rs9535670	ITM2B	cis	cerebellum	SCAN
rs9535670	HNRNPA1L2	cis	cerebellum	SCAN
rs9535670	CKAP2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52028000-52029600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr13:52028000-52029800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr13:52028400-52029600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:52028400-52029600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:52028400-52029600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:52028400-52029600	Weak transcription	Esophagus	oesophagus
7	chr13:52028400-52029600	Weak transcription	Gastric	stomach
8	chr13:52028400-52029600	Weak transcription	Ovary	ovary
9	chr13:52028400-52029600	Weak transcription	Pancreas	Pancrea
10	chr13:52028400-52029600	Weak transcription	Spleen	Spleen
11	chr13:52028400-52029800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:52028400-52029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr13:52028400-52030200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:52028600-52029600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:52028600-52029600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:52028600-52029600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:52028600-52029600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:52028600-52029600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr13:52028600-52029600	Weak transcription	Left Ventricle	heart
20	chr13:52028600-52029600	Weak transcription	Lung	lung
21	chr13:52028600-52029600	Weak transcription	Right Ventricle	heart
22	chr13:52028600-52029800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:52028600-52029800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:52028600-52029800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:52028600-52029800	Weak transcription	Colonic Mucosa	Colon
26	chr13:52028600-52029800	Weak transcription	Placenta	Placenta
27	chr13:52028600-52030000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr13:52028600-52030200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr13:52028600-52030200	Weak transcription	HSMM	muscle
30	chr13:52028600-52030400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr13:52028600-52030400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:52028600-52030400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr13:52028600-52032200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr13:52028600-52034000	Weak transcription	Aorta	Aorta
35	chr13:52028600-52036000	Weak transcription	HSMMtube	muscle
36	chr13:52028800-52029600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:52028800-52029600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr13:52028800-52029600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr13:52028800-52029600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:52028800-52029600	Enhancers	Colon Smooth Muscle	Colon
41	chr13:52028800-52029600	Weak transcription	Fetal Muscle Leg	muscle
42	chr13:52028800-52029600	Weak transcription	Fetal Stomach	stomach
43	chr13:52028800-52029800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr13:52028800-52030000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr13:52028800-52030800	ZNF genes & repeats	Dnd41	blood
46	chr13:52028800-52031000	ZNF genes & repeats	Fetal Thymus	thymus
47	chr13:52028800-52031600	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr13:52028800-52032000	Weak transcription	Osteobl	bone
49	chr13:52029000-52029600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr13:52029000-52029600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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