Variant report

Variant	rs2061508
Chromosome Location	chr4:75124840-75124841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:75124334..75127975-chr4:75147199..75149454,4	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10009707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010575	0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs10013212	0.91[EUR][1000 genomes]
rs10017409	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]
rs10017417	0.84[EUR][1000 genomes]
rs10018373	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs10019396	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs10023519	0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs10026687	0.87[EUR][1000 genomes]
rs10028285	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037824	0.94[EUR][1000 genomes]
rs10433673	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10938112	0.90[EUR][1000 genomes]
rs11724468	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737662	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1246575	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1246577	0.84[EUR][1000 genomes]
rs1246578	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1246579	0.82[EUR][1000 genomes]
rs1246580	0.81[EUR][1000 genomes]
rs1246582	0.84[EUR][1000 genomes]
rs1246584	0.84[EUR][1000 genomes]
rs1246586	0.84[EUR][1000 genomes]
rs1246587	0.84[EUR][1000 genomes]
rs1246588	0.84[EUR][1000 genomes]
rs1246590	0.82[EUR][1000 genomes]
rs1246591	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1246597	0.81[EUR][1000 genomes]
rs12500697	0.81[EUR][1000 genomes]
rs1265327	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs13116896	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13142241	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1371796	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1371797	0.88[CHB][hapmap]
rs1380561	0.87[EUR][1000 genomes]
rs1460016	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1460017	0.81[EUR][1000 genomes]
rs16850862	0.95[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]
rs16850883	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs17232394	0.87[EUR][1000 genomes]
rs17829765	0.89[TSI][hapmap]
rs1964526	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2045616	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2045617	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs2045618	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2367555	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2367745	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378517	0.89[EUR][1000 genomes]
rs28436705	0.91[EUR][1000 genomes]
rs28539097	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28644493	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695994	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4371587	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4502653	0.87[EUR][1000 genomes]
rs4577545	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694184	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488440	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs58813617	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62312513	0.84[EUR][1000 genomes]
rs62312515	0.87[EUR][1000 genomes]
rs62312545	0.86[EUR][1000 genomes]
rs6446983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446984	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6446985	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6814880	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6819605	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820992	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs6821664	0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6835734	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6854203	0.86[EUR][1000 genomes]
rs6854723	0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs715844	0.82[EUR][1000 genomes]
rs7659389	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7663269	0.87[ASW][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7665105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7670535	0.88[EUR][1000 genomes]
rs7672588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681137	0.88[CHB][hapmap]
rs7681912	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7683181	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9992393	0.87[EUR][1000 genomes]
rs9997322	0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9997788	0.82[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1002907	chr4:75013441-75131443	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	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
rs2061508	CNOT6L	cis	parietal	SCAN
rs2061508	ANKRD56	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75119600-75125000	Weak transcription	Lung	lung
2	chr4:75119800-75125000	Weak transcription	Pancreas	Pancrea
3	chr4:75119800-75125800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:75119800-75133200	Weak transcription	NHEK	skin
5	chr4:75119800-75148800	Weak transcription	Aorta	Aorta
6	chr4:75120000-75141200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:75121800-75125200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:75122600-75126400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:75123800-75131000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:75124000-75125200	Enhancers	Stomach Mucosa	stomach
11	chr4:75124000-75125600	Enhancers	Fetal Heart	heart
12	chr4:75124200-75133600	Weak transcription	Primary T cells from cord blood	blood
13	chr4:75124600-75125200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:75124600-75125400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:75124800-75125000	Enhancers	Right Ventricle	heart
16	chr4:75124800-75125200	Enhancers	Left Ventricle	heart
17	chr4:75124800-75125200	Enhancers	K562	blood
18	chr4:75124800-75126000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:75124800-75126000	Enhancers	Esophagus	oesophagus
20	chr4:75124800-75126400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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