Variant report

Variant	rs10017409
Chromosome Location	chr4:75162678-75162679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:75155655..75159395-chr4:75160422..75166473,8	K562	blood:
2	chr4:75067335..75068932-chr4:75162258..75164464,2	MCF-7	breast:
3	chr4:75161899..75164379-chr4:75195063..75196891,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10009707	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10010575	0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs10013212	0.90[EUR][1000 genomes]
rs10017417	0.82[EUR][1000 genomes]
rs10018373	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10019396	0.91[EUR][1000 genomes]
rs10023519	0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs10026687	0.90[EUR][1000 genomes]
rs10028285	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1037824	0.97[EUR][1000 genomes]
rs10433673	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938112	0.91[EUR][1000 genomes]
rs11724468	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737662	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1246575	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs1246577	0.82[EUR][1000 genomes]
rs1246578	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs1246579	0.80[EUR][1000 genomes]
rs1246582	0.82[EUR][1000 genomes]
rs1246584	0.82[EUR][1000 genomes]
rs1246586	0.82[EUR][1000 genomes]
rs1246587	0.82[EUR][1000 genomes]
rs1246588	0.82[EUR][1000 genomes]
rs1246590	0.80[EUR][1000 genomes]
rs1246591	0.87[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12500697	0.81[EUR][1000 genomes]
rs1265327	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs13116896	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142241	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1371796	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1371797	0.88[CHB][hapmap]
rs1380561	0.85[EUR][1000 genomes]
rs1460016	0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16850862	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850883	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs17232394	0.90[EUR][1000 genomes]
rs17829765	0.89[TSI][hapmap]
rs1964526	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045616	0.91[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2045617	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs2045618	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2061508	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2367555	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2367745	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378517	0.87[EUR][1000 genomes]
rs28436705	0.89[EUR][1000 genomes]
rs28539097	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28644493	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28695994	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4371587	0.88[EUR][1000 genomes]
rs4502653	0.90[EUR][1000 genomes]
rs4577545	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4694184	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488440	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs58813617	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62312513	0.82[EUR][1000 genomes]
rs62312515	0.85[EUR][1000 genomes]
rs62312545	0.89[EUR][1000 genomes]
rs6446983	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446984	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446985	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6814880	0.91[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6819605	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820992	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs6821664	0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs6835734	0.91[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6854203	0.84[EUR][1000 genomes]
rs6854723	0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs715844	0.85[EUR][1000 genomes]
rs7659389	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7663269	0.88[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7665105	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7670535	0.89[EUR][1000 genomes]
rs7672588	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681137	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs7681912	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7683181	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9992393	0.85[EUR][1000 genomes]
rs9997322	0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs9997788	0.88[EUR][1000 genomes]

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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10017409	CNOT6L	cis	parietal	SCAN
rs10017409	ANKRD56	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75134000-75173800	Weak transcription	Primary T cells from cord blood	blood
2	chr4:75149800-75186200	Weak transcription	K562	blood
3	chr4:75151400-75164600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:75156600-75165400	Weak transcription	Psoas Muscle	Psoas
5	chr4:75156600-75174200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:75159600-75170200	Weak transcription	NHEK	skin
7	chr4:75160200-75173800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:75160800-75168400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:75161200-75165400	Weak transcription	Fetal Kidney	kidney
10	chr4:75161600-75163600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:75162000-75162800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:75162000-75163400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links