Variant report

Variant	rs1868107
Chromosome Location	chr3:160611475-160611476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap]
rs10433352	0.81[CEU][hapmap]
rs11711152	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713093	0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs11717272	0.90[CEU][hapmap]
rs11718966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916355	0.84[EUR][1000 genomes]
rs11922296	0.81[JPT][hapmap]
rs13071999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13073059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13256	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs13315565	0.94[CEU][hapmap]
rs1345156	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1348976	0.81[JPT][hapmap]
rs1374789	0.81[JPT][hapmap]
rs1374790	0.81[JPT][hapmap]
rs1447610	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1447615	0.81[JPT][hapmap]
rs1447622	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562464	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs16831563	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16831796	0.81[CEU][hapmap]
rs1839016	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1839018	0.81[JPT][hapmap]
rs1868105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1868108	0.80[CHD][hapmap];0.88[GIH][hapmap]
rs1868109	0.81[JPT][hapmap]
rs2044571	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2197700	0.84[EUR][1000 genomes]
rs2889390	0.85[JPT][hapmap]
rs35257491	0.84[EUR][1000 genomes]
rs4679920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441337	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66872845	0.81[EUR][1000 genomes]
rs6768115	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6774725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801330	0.81[JPT][hapmap]
rs6801444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624185	1.00[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs7628389	0.81[CEU][hapmap]
rs7641892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898677	0.81[CEU][hapmap]
rs935497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs956447	0.81[JPT][hapmap]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap]
rs9822435	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs9832109	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs9844267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9845943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9857482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9857855	0.84[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs9871801	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs9881807	0.84[CHD][hapmap];0.91[GIH][hapmap]
rs9883566	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.82[TSI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1868107	PPM1L	cis	cerebellum	SCAN
rs1868107	B3GALNT1	cis	lymphoblastoid	seeQTL
rs1868107	C3orf57	cis	parietal	SCAN
rs1868107	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160604400-160616600	Weak transcription	Psoas Muscle	Psoas
2	chr3:160610800-160611600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:160610800-160611600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr3:160610800-160611600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr3:160610800-160612200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:160610800-160612200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:160610800-160612400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:160611000-160612200	Enhancers	Fetal Brain Female	brain
9	chr3:160611200-160615200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:160611200-160619400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:160611400-160611600	Enhancers	Fetal Brain Male	brain
12	chr3:160611400-160615200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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