Variant report

Variant	rs12301872
Chromosome Location	chr12:12561988-12561989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459099	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10505766	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs10743984	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10743986	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10743987	1.00[CHB][hapmap]
rs10772558	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772560	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10772561	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772562	0.81[AMR][1000 genomes]
rs10772564	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10772565	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10845531	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845534	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10845535	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10845536	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10845538	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10845549	1.00[JPT][hapmap]
rs10845550	1.00[CHB][hapmap]
rs11054874	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs11054879	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054885	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054895	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054898	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054900	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11054902	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11054904	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11054917	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11054918	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs11531025	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11537452	0.94[ASN][1000 genomes]
rs11559836	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16907998	1.00[YRI][hapmap]
rs2111270	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2417186	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918115	1.00[CHB][hapmap]
rs9645752	0.80[MEX][hapmap]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12301872	TAS2R31	cis	parietal	SCAN
rs12301872	LOH12CR1	cis	parietal	SCAN
rs12301872	ETV6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
2	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
3	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
4	chr12:12557200-12572400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:12557800-12565000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
7	chr12:12559200-12564800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:12559400-12564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:12560200-12562200	Weak transcription	Fetal Intestine Small	intestine
10	chr12:12560200-12564800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:12560200-12564800	Weak transcription	HepG2	liver
12	chr12:12561000-12562000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:12561000-12562000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr12:12561000-12562000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:12561000-12562000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr12:12561000-12562000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:12561000-12562200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:12561200-12562000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:12561200-12562000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:12561200-12562000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:12561200-12562200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:12561400-12562000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:12561400-12562000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr12:12561400-12562000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:12561600-12562200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:12561600-12562400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:12561600-12562600	Weak transcription	Brain Substantia Nigra	brain
28	chr12:12561800-12562000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:12561800-12562000	Enhancers	Dnd41	blood
30	chr12:12561800-12562000	Flanking Active TSS	GM12878-XiMat	blood

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