Variant report

Variant	rs10840170
Chromosome Location	chr11:9117898-9117899
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	chr11:9109432..9111291-chr11:9117498..9119505,2	K562	blood:
2	chr11:9109535..9113708-chr11:9115640..9120311,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264984	Chromatin interaction
ENSG00000175356	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10840171	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10840186	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840188	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10840189	1.00[JPT][hapmap]
rs11042179	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042190	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042191	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042192	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042196	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042197	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042201	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042215	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11042217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11042231	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11042232	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11042253	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11042268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1136966	1.00[CHB][hapmap]
rs11607384	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11827186	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360767	0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12363839	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs12366113	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17257379	1.00[JPT][hapmap]
rs1909215	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984775	1.00[CHB][hapmap]
rs2133215	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2173406	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653574	1.00[CHB][hapmap]
rs4061640	1.00[CHB][hapmap]
rs4910443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55948618	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57514354	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67988043	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7113467	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129049	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs72857949	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857989	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857991	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857993	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72857997	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7396115	1.00[CHB][hapmap]
rs7396130	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7396541	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7396840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929621	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7936201	1.00[CHB][hapmap]
rs7936622	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs7941341	1.00[CHB][hapmap]
rs7945759	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949022	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949349	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv467704	chr11:9059192-9125301	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv553454	chr11:9059192-9125301	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv982981	chr11:9115563-9121351	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10840170	TMEM41B	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9118600	Weak transcription	Right Atrium	heart
2	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
3	chr11:9114200-9122000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:9114200-9136200	Weak transcription	Fetal Heart	heart
5	chr11:9115000-9141800	Weak transcription	HSMM	muscle
6	chr11:9115200-9134400	Weak transcription	Fetal Stomach	stomach
7	chr11:9115800-9121800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:9116200-9118400	Weak transcription	Pancreas	Pancrea
9	chr11:9117600-9119200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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