Variant report

Variant	rs10819634
Chromosome Location	chr9:101860076-101860077
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	chr9:101858348..101860739-chr9:101862430..101863994,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1013186	0.83[EUR][1000 genomes]
rs10283455	0.96[TSI][hapmap]
rs10733709	0.91[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10739779	0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10760667	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10760668	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10760669	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10760670	1.00[ASW][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10760671	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10760672	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10760673	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10819635	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10819637	0.84[EUR][1000 genomes]
rs10819638	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10819640	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs10988703	0.86[EUR][1000 genomes]
rs10988706	1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10988709	1.00[CHB][hapmap]
rs10988714	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs10988715	1.00[CHB][hapmap]
rs10988716	1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10988717	1.00[CHB][hapmap]
rs10988723	0.81[AMR][1000 genomes]
rs11568752	1.00[CHB][hapmap]
rs11568753	0.87[CHB][hapmap]
rs11568770	0.91[CHB][hapmap]
rs11568778	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs12346650	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12685571	1.00[CHB][hapmap]
rs12686782	0.92[ASN][1000 genomes]
rs13286149	0.94[EUR][1000 genomes]
rs1571589	0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1571590	0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs1590	0.88[ASW][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap]
rs1626340	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1699413	0.90[AMR][1000 genomes]
rs1888223	0.80[ASN][1000 genomes]
rs1888225	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2026811	1.00[ASW][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs334348	0.88[ASW][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs334349	0.93[ASW][hapmap];0.90[LWK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs334351	0.80[ASN][1000 genomes]
rs334353	0.87[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs334354	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs334355	1.00[ASW][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs334356	0.96[TSI][hapmap]
rs334357	0.96[TSI][hapmap]
rs334362	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs367568	0.88[AMR][1000 genomes]
rs3739798	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs401186	0.88[AMR][1000 genomes]
rs420549	0.93[TSI][hapmap]
rs44466	0.83[AMR][1000 genomes]
rs597457	1.00[CHB][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6478972	1.00[ASW][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6478973	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7031302	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7031309	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7041311	0.91[CHB][hapmap]
rs7042852	0.91[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap]
rs7043624	0.82[CHB][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7874221	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs868	0.93[TSI][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	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10819634	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101854600-101860400	Enhancers	K562	blood
2	chr9:101855800-101861400	Weak transcription	Dnd41	blood
3	chr9:101856200-101861400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr9:101856200-101866200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:101856400-101860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:101856400-101861400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:101856400-101861600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:101856400-101861600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:101856400-101865600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:101856400-101865800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:101856400-101865800	Weak transcription	Placenta	Placenta
12	chr9:101858000-101863400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr9:101858200-101866000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:101858400-101860200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:101858800-101866200	Weak transcription	Primary T cells from cord blood	blood
16	chr9:101859400-101863200	Weak transcription	Fetal Thymus	thymus
17	chr9:101859400-101866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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