Variant report

Variant	rs1839018
Chromosome Location	chr3:160619361-160619362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160281146..160283028-chr3:160617867..160619821,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1045448	0.89[CEU][hapmap]
rs11711152	0.81[JPT][hapmap]
rs11713093	0.84[JPT][hapmap]
rs11718966	0.81[JPT][hapmap]
rs11922296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12107243	0.89[CEU][hapmap]
rs12488621	0.85[CEU][hapmap]
rs12494133	1.00[CEU][hapmap]
rs12696110	0.85[GIH][hapmap]
rs13071999	0.81[JPT][hapmap]
rs13073059	0.81[JPT][hapmap]
rs13079241	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13325518	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs1348976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1374789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1374795	0.95[JPT][hapmap]
rs1447610	0.81[JPT][hapmap]
rs1447615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1447622	0.90[JPT][hapmap]
rs16831868	0.89[CEU][hapmap]
rs1868106	0.83[GIH][hapmap]
rs1868107	0.81[JPT][hapmap]
rs1868109	0.90[JPT][hapmap]
rs1947686	0.89[CEU][hapmap]
rs2231252	0.89[CEU][hapmap]
rs2279106	0.89[CEU][hapmap]
rs4443220	0.89[CEU][hapmap]
rs4465984	0.84[CEU][hapmap]
rs4679917	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4679918	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679920	0.85[JPT][hapmap]
rs6441338	0.81[JPT][hapmap]
rs6441353	0.89[CEU][hapmap]
rs6763838	0.85[CEU][hapmap]
rs6768115	0.81[JPT][hapmap]
rs6774725	0.81[JPT][hapmap]
rs6776120	0.87[GIH][hapmap]
rs6791327	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6795977	0.89[CEU][hapmap]
rs6799779	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6801330	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7429731	0.85[CEU][hapmap]
rs7630896	0.85[CEU][hapmap]
rs7641892	0.81[JPT][hapmap]
rs7649954	0.85[CEU][hapmap]
rs898683	0.85[CEU][hapmap]
rs898684	0.85[CEU][hapmap]
rs898685	0.84[CEU][hapmap]
rs935497	0.81[JPT][hapmap]
rs956447	0.90[JPT][hapmap]
rs9824308	0.85[CEU][hapmap]
rs9844267	0.81[JPT][hapmap]
rs9857195	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9857482	0.80[JPT][hapmap]
rs9861850	0.89[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3391648	chr3:160602299-160620598	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1839018	C3orf57	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160611200-160619400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:160615800-160620800	Weak transcription	Fetal Brain Male	brain
3	chr3:160616600-160627600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160617200-160620800	Weak transcription	Psoas Muscle	Psoas
5	chr3:160618600-160619600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:160618600-160619600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:160618800-160619400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:160618800-160619600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:160619000-160619400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:160619000-160619400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:160619000-160619600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:160619000-160619600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:160619200-160619600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:160619200-160619600	Enhancers	HUES6 Cell Line	embryonic stem cell

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