Variant report

Variant	rs334366
Chromosome Location	chr9:101929237-101929238
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101921262..101923800-chr9:101929228..101931291,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1013186	0.94[CEU][hapmap]
rs10283455	0.94[CEU][hapmap]
rs10448292	0.83[EUR][1000 genomes]
rs10733708	0.83[ASN][1000 genomes]
rs10733709	0.94[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10739778	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10739779	0.94[CEU][hapmap];0.81[LWK][hapmap]
rs10760668	0.93[ASN][1000 genomes]
rs10760669	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10760670	0.89[CEU][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10760671	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10760672	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10760673	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10760674	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10819636	0.91[ASN][1000 genomes]
rs10819638	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10819639	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10819640	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs10988706	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10988709	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10988715	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10988716	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10988717	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10988723	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11568752	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs11568753	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs11568770	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs11568778	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs12345675	0.89[EUR][1000 genomes]
rs12346650	0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs12685571	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1571589	0.89[CEU][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1571590	0.94[CEU][hapmap]
rs1590	0.95[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1626340	0.81[ASN][1000 genomes]
rs1699413	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1888225	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[ASN][1000 genomes]
rs1973518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026811	0.89[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs334348	0.95[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334349	0.95[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334351	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334353	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs334354	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs334355	0.89[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs334356	0.94[CEU][hapmap]
rs334357	0.94[CEU][hapmap]
rs334358	0.94[CEU][hapmap]
rs334362	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs334363	1.00[ASN][1000 genomes]
rs334364	1.00[ASN][1000 genomes]
rs334365	0.86[ASN][1000 genomes]
rs334367	1.00[ASN][1000 genomes]
rs334368	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs334369	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs334370	0.98[ASN][1000 genomes]
rs334371	0.85[ASN][1000 genomes]
rs367568	0.83[ASN][1000 genomes]
rs3739798	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[ASN][1000 genomes]
rs383496	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs401186	0.83[ASN][1000 genomes]
rs420549	0.94[CEU][hapmap];0.84[LWK][hapmap]
rs44466	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs478061	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs597457	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6478972	0.89[CEU][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6478973	0.95[ASN][1000 genomes]
rs7031302	0.82[CEU][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7031309	0.83[ASN][1000 genomes]
rs7041311	0.91[CHB][hapmap]
rs7042852	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7043624	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7874221	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs868	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs334366	TGFBR1	cis	cerebellum	SCAN
rs334366	LOC286359	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101912600-101932200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:101914800-101929800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr9:101916000-101929600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:101922400-101930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:101922600-101930600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:101922800-101930000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:101922800-101932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:101925200-101929400	Weak transcription	K562	blood
9	chr9:101925400-101930000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:101925800-101929600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:101926400-101930800	Enhancers	GM12878-XiMat	blood
12	chr9:101927800-101930800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr9:101928000-101930400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:101928400-101930800	Enhancers	Primary T cells from cord blood	blood
15	chr9:101928800-101929400	Weak transcription	Thymus	Thymus
16	chr9:101928800-101930800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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