Variant report

Variant	rs9535663
Chromosome Location	chr13:51997092-51997093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51996691..52002238-chr13:52025569..52028541,7	MCF-7	breast:
2	chr13:51995533..51997582-chr13:52026152..52028042,2	K562	blood:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1028727	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12860899	1.00[LWK][hapmap]
rs17075688	0.80[EUR][1000 genomes]
rs17194948	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17195020	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026526	0.90[ASN][1000 genomes]
rs2277443	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs2408363	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap]
rs4555048	1.00[ASW][hapmap]
rs4628860	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4943003	1.00[ASW][hapmap]
rs56017742	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561638	1.00[ASW][hapmap]
rs73197809	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73197821	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73197824	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7321642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7328715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335122	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7335144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7337450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7989850	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[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7998084	0.90[CEU][hapmap]
rs8001311	0.80[EUR][1000 genomes]
rs9316541	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316545	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316546	0.90[ASN][1000 genomes]
rs9526757	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs9526758	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526764	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535625	1.00[LWK][hapmap]
rs9535640	0.83[EUR][1000 genomes]
rs9535646	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535660	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535670	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]
rs9535671	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535672	0.80[EUR][1000 genomes]
rs9535677	0.80[EUR][1000 genomes]
rs9535678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535679	0.80[EUR][1000 genomes]
rs9535680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535682	0.98[ASN][1000 genomes]
rs9535683	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535689	0.88[ASN][1000 genomes]
rs9535694	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9535696	0.89[CEU][hapmap]
rs9535697	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs9535699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9535717	1.00[ASW][hapmap]
rs9563046	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568600	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9568603	0.90[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs9568612	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs9634842	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535663	ITM2B	cis	cerebellum	SCAN
rs9535663	CKAP2	cis	parietal	SCAN
rs9535663	WDFY2	cis	parietal	SCAN
rs9535663	DDX26	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51945800-52016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:51950200-51999800	Weak transcription	Brain Germinal Matrix	brain
5	chr13:51963200-52024800	Weak transcription	Fetal Intestine Large	intestine
6	chr13:51963600-52003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr13:51971800-52025000	Weak transcription	Fetal Stomach	stomach
8	chr13:51972000-51999400	Weak transcription	Small Intestine	intestine
9	chr13:51972000-52005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:51972000-52016000	Weak transcription	Pancreas	Pancrea
11	chr13:51978400-52003200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:51981600-51999400	Weak transcription	Brain Angular Gyrus	brain
13	chr13:51984400-52024800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr13:51985000-51999400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr13:51988200-52001000	Weak transcription	Aorta	Aorta
16	chr13:51988600-51999400	Weak transcription	Brain Anterior Caudate	brain
17	chr13:51988600-51999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:51988800-51999400	Weak transcription	Brain Hippocampus Middle	brain
19	chr13:51988800-52024400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:51989800-51997800	Strong transcription	HSMM	muscle
21	chr13:51990000-51997200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:51990000-52016600	Weak transcription	Fetal Intestine Small	intestine
23	chr13:51990800-51999800	Weak transcription	Fetal Brain Female	brain
24	chr13:51990800-52003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr13:51991200-51999400	Weak transcription	NHLF	lung
26	chr13:51991200-51999800	Weak transcription	A549	lung
27	chr13:51991400-52003200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:51991400-52006200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr13:51992400-51998000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr13:51992400-52025400	Weak transcription	Esophagus	oesophagus
31	chr13:51992600-52002200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr13:51992800-51998000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr13:51993000-52002200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:51993600-51999800	Weak transcription	Fetal Lung	lung
35	chr13:51993600-52003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr13:51993800-52001200	Weak transcription	NH-A	brain
37	chr13:51994000-51999400	Weak transcription	Colon Smooth Muscle	Colon
38	chr13:51994200-51999200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr13:51994600-51997800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:51994600-52002200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:51994600-52005600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr13:51994800-51998200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr13:51995000-51997600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr13:51995000-51997600	Enhancers	Fetal Heart	heart
45	chr13:51995000-51997600	Strong transcription	K562	blood
46	chr13:51995000-51997800	Weak transcription	Colonic Mucosa	Colon
47	chr13:51995000-51998000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr13:51995000-51998000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:51995000-51998200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr13:51995000-51998800	Genic enhancers	HUES64 Cell Line	embryonic stem cell

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