Variant report

Variant	rs12901929
Chromosome Location	chr15:49675308-49675309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10519224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10519225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10851478	1.00[YRI][hapmap]
rs11070706	0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11853969	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11854039	1.00[AFR][1000 genomes]
rs11854557	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11855798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11858411	0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12050614	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12148764	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12232355	0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs12591300	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592508	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12595692	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs12901353	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12902096	0.80[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12902271	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12905203	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905477	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12908624	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12908635	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12912703	0.82[CHB][hapmap]
rs12914876	0.88[AFR][1000 genomes]
rs12916839	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1395901	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs17402115	0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs17435932	1.00[AFR][1000 genomes]
rs17478694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17478785	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17479589	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1911612	0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1961393	1.00[AFR][1000 genomes]
rs2899434	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs34562714	1.00[AFR][1000 genomes]
rs34748066	1.00[AFR][1000 genomes]
rs36023246	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36100631	1.00[AFR][1000 genomes]
rs4389093	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4436732	0.84[AFR][1000 genomes]
rs4480740	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4547278	0.84[AFR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes]
rs4775806	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes]
rs62009834	1.00[AFR][1000 genomes]
rs62009977	0.84[AFR][1000 genomes]
rs6493372	0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7174135	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs7180168	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7497335	0.92[AFR][1000 genomes]
rs8029687	0.82[AFR][1000 genomes]
rs9920722	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv442375	chr15:49652524-49684082	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12901929	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49670800-49675400	Weak transcription	NHLF	lung
2	chr15:49673400-49675400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:49673400-49675400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:49673400-49676000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:49673400-49676200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:49673600-49675400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:49673600-49676000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:49673600-49676200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:49673800-49683400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:49674400-49677400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr15:49674600-49676400	Enhancers	Hela-S3	cervix
12	chr15:49674800-49675400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr15:49674800-49675800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:49675000-49675400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr15:49675000-49675600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:49675200-49675600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:49675200-49676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:49675200-49676400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links