Variant report

Variant	rs16867498
Chromosome Location	chr2:182687021-182687022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182685284..182687547-chr2:182730899..182732753,2	MCF-7	breast:
2	chr2:182685989..182687787-chr2:182689846..182691417,2	MCF-7	breast:
3	chr2:182687016..182689280-chr2:182756224..182758607,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260742	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10165936	1.00[CEU][hapmap]
rs10166812	0.85[JPT][hapmap]
rs10166975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167581	0.83[YRI][hapmap]
rs10171629	0.81[AFR][1000 genomes]
rs10173114	1.00[CEU][hapmap]
rs10176061	1.00[CEU][hapmap]
rs10176613	1.00[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap]
rs10176757	1.00[CEU][hapmap]
rs10179363	1.00[CEU][hapmap]
rs10179547	1.00[CEU][hapmap]
rs10189187	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199645	1.00[CEU][hapmap]
rs10200243	1.00[CEU][hapmap]
rs10201303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203440	0.81[AFR][1000 genomes]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap]
rs13391733	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13396152	0.80[YRI][hapmap];0.85[AFR][1000 genomes]
rs13401364	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425734	1.00[CEU][hapmap]
rs1528024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867509	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17456384	0.87[EUR][1000 genomes]
rs1881158	1.00[CEU][hapmap]
rs1881159	1.00[CEU][hapmap]
rs2059702	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2288330	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2303554	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2368224	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2368235	0.92[EUR][1000 genomes]
rs3731693	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3815877	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3815878	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4597477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732891	0.84[EUR][1000 genomes]
rs55758877	0.87[EUR][1000 genomes]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6720109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720702	1.00[CEU][hapmap]
rs6723011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735322	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6736341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6744556	0.84[EUR][1000 genomes]
rs6748354	1.00[CEU][hapmap]
rs6751464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751685	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6754192	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6754819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755017	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs73032623	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7580410	1.00[CEU][hapmap]
rs7600976	0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs7603721	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7608942	1.00[CEU][hapmap]
rs9807949	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9808112	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16867498	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182682200-182695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:182686400-182687200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:182686400-182687800	Enhancers	Fetal Thymus	thymus
4	chr2:182687000-182690200	Weak transcription	Pancreas	Pancrea

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