Variant report

Variant	rs9876142
Chromosome Location	chr3:160780968-160780969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160485944..160487804-chr3:160779253..160781559,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10154889	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs10433352	0.81[MEX][hapmap];0.90[AMR][1000 genomes]
rs11711152	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs11712713	0.81[EUR][1000 genomes]
rs11715733	0.90[AMR][1000 genomes]
rs11717272	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11718966	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs11720263	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11915989	0.88[EUR][1000 genomes]
rs11922957	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11922959	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12696112	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12696113	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13060601	0.91[EUR][1000 genomes]
rs13060718	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13062651	0.85[AMR][1000 genomes]
rs13071892	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13071999	0.90[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs13073059	0.90[CEU][hapmap]
rs13085336	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs13098896	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13315565	0.94[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1345156	0.90[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs1447610	0.90[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs1447622	0.94[CEU][hapmap]
rs1562464	0.90[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1599388	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16831796	0.86[MEX][hapmap];0.93[AMR][1000 genomes]
rs16831886	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1868105	0.90[CEU][hapmap]
rs1868107	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs2014810	0.90[AMR][1000 genomes]
rs2044571	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs2889390	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs34221255	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34630898	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35127376	0.80[EUR][1000 genomes]
rs35914913	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4494975	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4521287	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4679920	0.90[CEU][hapmap]
rs4679929	0.87[AMR][1000 genomes]
rs4856700	0.90[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs57145341	0.93[AMR][1000 genomes]
rs6441338	0.94[CEU][hapmap];0.80[JPT][hapmap]
rs6441362	0.91[EUR][1000 genomes]
rs6768115	0.90[CEU][hapmap]
rs6772723	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6774725	0.90[CEU][hapmap]
rs6794882	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6801444	0.90[CEU][hapmap]
rs6806015	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs68166680	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73021215	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73023235	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7610432	0.90[AMR][1000 genomes]
rs7618924	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7624185	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7628389	0.81[MEX][hapmap];0.89[AMR][1000 genomes]
rs7641892	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs898677	0.81[MEX][hapmap];0.90[AMR][1000 genomes]
rs935497	0.90[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs964533	0.90[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9812507	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9822435	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9832109	0.90[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9844267	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs9845943	0.90[CEU][hapmap];0.93[GIH][hapmap]
rs9857482	0.90[CEU][hapmap]
rs9857855	0.90[AMR][1000 genomes]
rs9860537	0.90[CEU][hapmap];0.90[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9862086	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9880269	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9883566	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9876142	NMD3	cis	parietal	SCAN
rs9876142	SPTSSB	cis	Thyroid	GTEx
rs9876142	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs9876142	PPM1L	cis	cerebellum	SCAN
rs9876142	B3GALNT1	cis	lymphoblastoid	seeQTL
rs9876142	C3orf57	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160768000-160786400	Weak transcription	Left Ventricle	heart
3	chr3:160771000-160783200	Weak transcription	Fetal Brain Female	brain
4	chr3:160772000-160784200	Weak transcription	Primary B cells from cord blood	blood
5	chr3:160773200-160786800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:160773600-160785600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:160773800-160787200	Weak transcription	Gastric	stomach
8	chr3:160775800-160782600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:160776000-160787200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:160777200-160787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:160778200-160782600	Weak transcription	Esophagus	oesophagus
12	chr3:160778200-160786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:160779200-160785200	Weak transcription	Aorta	Aorta
14	chr3:160780400-160788600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:160780600-160786400	Weak transcription	Primary T cells from cord blood	blood
16	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain

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