Variant report

Variant	rs40062
Chromosome Location	chr5:107447121-107447122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10040007	1.00[CHB][hapmap]
rs10045002	1.00[CHB][hapmap]
rs10070927	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10071499	1.00[CHB][hapmap]
rs158171	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs158174	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs158176	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158177	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158178	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158180	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs158182	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158183	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158184	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs158185	0.90[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158187	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158189	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs169640	0.91[CHD][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs171756	1.00[CHB][hapmap]
rs192617	0.82[EUR][1000 genomes]
rs286740	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs286742	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs286748	0.91[CHD][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs286752	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs286757	0.82[EUR][1000 genomes]
rs286763	0.84[ASN][1000 genomes]
rs286778	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs286783	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs286786	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs286788	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs286790	0.84[EUR][1000 genomes]
rs286796	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs286797	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs286798	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs286801	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs286803	0.94[EUR][1000 genomes]
rs286804	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286807	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286810	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286814	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs286816	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs286819	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs288130	0.82[EUR][1000 genomes]
rs288140	0.91[CHD][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs288148	0.82[EUR][1000 genomes]
rs288150	0.82[EUR][1000 genomes]
rs288153	0.83[EUR][1000 genomes]
rs288155	0.83[EUR][1000 genomes]
rs288156	0.82[EUR][1000 genomes]
rs288158	0.81[EUR][1000 genomes]
rs288162	0.83[EUR][1000 genomes]
rs288163	0.83[EUR][1000 genomes]
rs288165	0.81[EUR][1000 genomes]
rs288166	0.81[EUR][1000 genomes]
rs288167	0.82[EUR][1000 genomes]
rs288174	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs288176	1.00[CHB][hapmap]
rs288182	0.90[CHD][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs289234	0.83[EUR][1000 genomes]
rs2909879	0.91[CHD][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2909880	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2909882	0.91[CHD][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2910791	1.00[CHB][hapmap]
rs2922408	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2922425	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2922431	1.00[CHB][hapmap]
rs2966788	1.00[CHB][hapmap]
rs2966800	1.00[CHB][hapmap]
rs2966803	1.00[CHB][hapmap]
rs2966820	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2966821	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2966823	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2966825	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs2966827	0.84[ASN][1000 genomes]
rs2966828	0.90[CHD][hapmap]
rs2966829	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs34386	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[TSI][hapmap]
rs34387	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34411	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34416	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34417	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs34418	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34426	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34429	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40063	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40065	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs40066	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs40072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41130	0.81[AMR][1000 genomes]
rs4395619	0.84[ASN][1000 genomes]
rs455394	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4957551	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs502790	0.91[CHD][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs6594295	1.00[CHB][hapmap]
rs6880727	1.00[CHB][hapmap]
rs7706429	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs7727051	1.00[CHB][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	nsv882682	chr5:107213361-107458336	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv534281	chr5:107357579-107674981	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107388400-107510800	Weak transcription	Primary B cells from cord blood	blood
2	chr5:107437800-107447600	Weak transcription	Right Atrium	heart
3	chr5:107437800-107463800	Weak transcription	Esophagus	oesophagus
4	chr5:107438400-107447600	Weak transcription	Pancreas	Pancrea
5	chr5:107438400-107448800	Weak transcription	Left Ventricle	heart
6	chr5:107440600-107450200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:107441200-107455000	Weak transcription	Psoas Muscle	Psoas
8	chr5:107441800-107457400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:107445400-107448000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:107445600-107447400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:107445600-107447600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:107445800-107447600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:107446200-107447200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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