Variant report

Variant	rs16865846
Chromosome Location	chr2:178717517-178717518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10164920	1.00[JPT][hapmap]
rs10165089	1.00[JPT][hapmap]
rs10168605	1.00[JPT][hapmap]
rs10170290	1.00[JPT][hapmap]
rs10170607	1.00[JPT][hapmap]
rs10170914	1.00[CEU][hapmap]
rs10171486	1.00[JPT][hapmap]
rs10174604	1.00[JPT][hapmap]
rs10181377	1.00[JPT][hapmap]
rs10183144	1.00[JPT][hapmap]
rs10186239	1.00[JPT][hapmap]
rs10190066	1.00[JPT][hapmap]
rs10190805	1.00[JPT][hapmap]
rs10191328	1.00[JPT][hapmap]
rs10193299	1.00[JPT][hapmap]
rs10194612	1.00[JPT][hapmap]
rs10198681	1.00[JPT][hapmap]
rs10198877	1.00[JPT][hapmap]
rs10208501	1.00[JPT][hapmap]
rs10211341	1.00[JPT][hapmap]
rs10221783	1.00[JPT][hapmap]
rs10497483	1.00[JPT][hapmap]
rs10930817	1.00[JPT][hapmap]
rs12151755	1.00[JPT][hapmap]
rs12693128	1.00[JPT][hapmap]
rs12693133	1.00[JPT][hapmap]
rs12995449	1.00[JPT][hapmap]
rs13003683	1.00[JPT][hapmap]
rs13008170	1.00[JPT][hapmap]
rs13008780	1.00[JPT][hapmap]
rs13009350	1.00[JPT][hapmap]
rs13015148	1.00[JPT][hapmap]
rs13386418	1.00[JPT][hapmap]
rs13400109	1.00[JPT][hapmap]
rs13400411	1.00[JPT][hapmap]
rs13410185	1.00[JPT][hapmap]
rs13411527	1.00[JPT][hapmap]
rs13411542	1.00[JPT][hapmap]
rs13411922	1.00[JPT][hapmap]
rs13411970	1.00[JPT][hapmap]
rs13412181	1.00[CEU][hapmap]
rs13413095	1.00[JPT][hapmap]
rs13413731	1.00[JPT][hapmap]
rs13419437	1.00[JPT][hapmap]
rs13422276	1.00[JPT][hapmap]
rs13425873	1.00[JPT][hapmap]
rs13428032	1.00[JPT][hapmap]
rs1527291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823484	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865786	0.83[EUR][1000 genomes]
rs16865818	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16865821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16865903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16865951	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs16866034	1.00[CEU][hapmap]
rs17329742	1.00[JPT][hapmap]
rs17329956	1.00[JPT][hapmap]
rs17401468	1.00[JPT][hapmap]
rs17401650	1.00[JPT][hapmap]
rs17401671	1.00[JPT][hapmap]
rs1898012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2015183	1.00[CEU][hapmap]
rs3770053	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821011	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs41357848	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs4377360	1.00[JPT][hapmap]
rs4423634	1.00[JPT][hapmap]
rs58297855	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717171	0.80[YRI][hapmap]
rs6733229	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561059	1.00[JPT][hapmap]
rs7578601	0.80[YRI][hapmap]
rs9288011	1.00[JPT][hapmap]
rs9646795	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv3053	chr2:178690640-178735132	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv978954	chr2:178716893-178719864	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3322845	chr2:178717331-178719879	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16865846	ICA1	trans	lymphoblastoid	RTeQTL
rs16865846	TAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178716600-178717800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:178716600-178718200	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr2:178716800-178717600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr2:178716800-178717600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:178716800-178718000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:178717000-178720600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:178717000-178720800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:178717400-178719400	Weak transcription	Adipose Nuclei	Adipose

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