Variant report

Variant	rs12475916
Chromosome Location	chr2:173414693-173414694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1076595	0.81[ASN][1000 genomes]
rs12465295	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465442	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12467358	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12469958	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12474168	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474995	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476126	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12477247	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477594	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12478465	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619242	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622687	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13383151	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13402061	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1344272	0.81[ASN][1000 genomes]
rs1574247	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16860543	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2178474	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293646	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2357415	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34094408	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3792257	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3792260	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4308101	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4619573	0.81[ASN][1000 genomes]
rs4972839	0.84[ASN][1000 genomes]
rs56084828	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57418091	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs57957394	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58016698	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58044442	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59020762	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59524026	0.84[ASN][1000 genomes]
rs59610589	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60275829	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60442917	0.84[ASN][1000 genomes]
rs60446415	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61542159	0.96[EUR][1000 genomes]
rs6718477	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6755100	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72894386	0.84[ASN][1000 genomes]
rs7564591	0.81[ASN][1000 genomes]
rs7564654	0.81[ASN][1000 genomes]
rs7565216	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7582972	0.81[ASN][1000 genomes]
rs7591883	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609465	0.81[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173392600-173419600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:173410000-173418800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:173410600-173417000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:173410800-173418000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:173410800-173418800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:173411000-173419600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:173411400-173417600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:173412800-173415800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:173413000-173415800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:173413000-173417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:173413000-173419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:173413000-173419600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:173413400-173416000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr2:173413400-173419200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr2:173413600-173415400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:173413600-173415800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:173413600-173415800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr2:173413600-173416000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr2:173413800-173414800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr2:173413800-173415600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:173413800-173416200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:173413800-173416800	Weak transcription	Primary B cells from cord blood	blood
23	chr2:173413800-173419800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:173414000-173415600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:173414000-173415600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:173414000-173416000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:173414000-173416400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:173414000-173416400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:173414000-173416600	Enhancers	Primary T cells from cord blood	blood
30	chr2:173414000-173417000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:173414000-173417200	Weak transcription	HMEC	breast
32	chr2:173414000-173418000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr2:173414000-173418000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr2:173414000-173419400	Weak transcription	Placenta	Placenta
35	chr2:173414200-173415400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:173414200-173415600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr2:173414200-173415800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:173414200-173415800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:173414400-173416800	Weak transcription	GM12878-XiMat	blood
40	chr2:173414600-173415000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr2:173414600-173415400	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:173414600-173415600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:173414600-173417600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:173414600-173419000	Weak transcription	Primary T cells fromperipheralblood	blood

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