Variant report

Variant	rs2252664
Chromosome Location	chr12:10786797-10786798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10771079..10773905-chr12:10786792..10788770,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10431297	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1073305	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs10772339	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10772340	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs10772343	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs10772347	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1078437	0.81[MEX][hapmap]
rs10845186	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10845187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845192	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs10845194	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs10845195	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs10845197	0.87[CEU][hapmap]
rs10845198	0.86[JPT][hapmap]
rs11053886	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12316690	0.91[CEU][hapmap]
rs12321017	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12582745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17742332	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1979268	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1993498	0.82[GIH][hapmap];0.93[JPT][hapmap];0.90[TSI][hapmap]
rs1993500	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2009908	0.95[ASN][1000 genomes]
rs2054194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054195	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168747	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2168748	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2277410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290717	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2418087	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs2418088	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs2418095	0.90[CEU][hapmap]
rs2900513	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs3759259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782671	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4763573	0.88[CEU][hapmap]
rs61912160	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61912161	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6488316	0.88[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7313620	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs7350557	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs7350597	0.88[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7968284	0.86[JPT][hapmap]
rs7970568	0.88[CEU][hapmap]
rs7971142	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs8181761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv607	chr12:10776867-10821535	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2252664	STYK1	cis	parietal	SCAN
rs2252664	COPS7A	cis	parietal	SCAN
rs2252664	TPI1	cis	parietal	SCAN
rs2252664	TAS2R20	cis	cerebellum	SCAN
rs2252664	TAS2R19	cis	cerebellum	SCAN
rs2252664	TAS2R14	cis	cerebellum	SCAN
rs2252664	TAS2R31	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10787000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:10766600-10789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10766600-10794400	Weak transcription	Gastric	stomach
4	chr12:10766800-10789400	Weak transcription	Esophagus	oesophagus
5	chr12:10772000-10787200	Weak transcription	NHEK	skin
6	chr12:10773000-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:10773400-10787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:10777600-10787400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:10779800-10790000	Strong transcription	HUVEC	blood vessel
10	chr12:10781000-10787000	Weak transcription	HMEC	breast
11	chr12:10782200-10787600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:10782200-10791000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:10782400-10789400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:10784000-10787000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:10784200-10787200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:10784200-10787800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:10784200-10788400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:10784800-10788800	Enhancers	NHDF-Ad	bronchial
19	chr12:10785200-10786800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:10785400-10786800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:10785400-10792600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:10785600-10787000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:10786200-10787000	Enhancers	Stomach Mucosa	stomach
24	chr12:10786200-10787000	Flanking Active TSS	HSMMtube	muscle
25	chr12:10786400-10787000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:10786400-10787200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr12:10786400-10787200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:10786400-10788000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:10786400-10788200	Enhancers	Placenta	Placenta
30	chr12:10786600-10786800	Enhancers	NHLF	lung
31	chr12:10786600-10787200	Strong transcription	Primary hematopoietic stem cells	blood
32	chr12:10786600-10787200	Flanking Active TSS	HSMM	muscle
33	chr12:10786600-10787600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:10786600-10788000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:10786600-10788000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:10786600-10788000	Enhancers	Osteobl	bone

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