Variant report

Variant	rs10176056
Chromosome Location	chr2:98918154-98918155
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98917651..98919589-chr2:98922274..98924651,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10181000	0.87[CHB][hapmap]
rs10190336	0.84[ASN][1000 genomes]
rs10199476	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs10201994	1.00[ASN][1000 genomes]
rs10202618	0.98[ASN][1000 genomes]
rs10203437	0.98[ASN][1000 genomes]
rs11124096	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs11124107	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11124121	0.87[ASN][1000 genomes]
rs11673807	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11679920	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11889349	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11891512	0.82[ASN][1000 genomes]
rs11895654	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs11901562	0.92[ASN][1000 genomes]
rs12470615	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs12478763	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12478769	0.82[ASN][1000 genomes]
rs12622324	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12624294	1.00[ASN][1000 genomes]
rs12712256	0.92[ASN][1000 genomes]
rs12993718	0.82[ASN][1000 genomes]
rs12999985	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13013876	0.82[ASN][1000 genomes]
rs13014142	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13033263	0.82[ASN][1000 genomes]
rs13394706	0.90[ASW][hapmap];0.87[CHB][hapmap]
rs13408372	0.85[CHB][hapmap]
rs13415414	1.00[ASN][1000 genomes]
rs13428221	0.83[ASN][1000 genomes]
rs1451251	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1466944	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs1504679	0.98[ASN][1000 genomes]
rs17427684	0.98[ASN][1000 genomes]
rs17428056	1.00[ASN][1000 genomes]
rs17429208	0.87[CHB][hapmap];0.83[MEX][hapmap]
rs17493655	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17493788	1.00[ASN][1000 genomes]
rs1875880	0.98[ASN][1000 genomes]
rs2102270	0.87[CHB][hapmap]
rs2122756	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs2202387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2221416	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2292118	0.87[CHB][hapmap]
rs2292119	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3731659	0.98[ASN][1000 genomes]
rs4374424	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs4389366	0.92[ASN][1000 genomes]
rs4455212	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs4477970	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4479470	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4494805	0.82[ASN][1000 genomes]
rs4535095	0.81[ASN][1000 genomes]
rs4608580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4632400	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4851122	0.92[ASN][1000 genomes]
rs4851123	0.98[ASN][1000 genomes]
rs4851124	0.98[ASN][1000 genomes]
rs4851935	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4851951	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4851952	0.82[ASN][1000 genomes]
rs4851954	0.94[ASN][1000 genomes]
rs4851955	0.98[ASN][1000 genomes]
rs4851959	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4851960	0.91[ASN][1000 genomes]
rs62157914	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6543419	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs6543459	1.00[ASN][1000 genomes]
rs66464436	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6715989	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6725543	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6742930	0.98[ASN][1000 genomes]
rs6747344	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6747410	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs6750975	0.98[ASN][1000 genomes]
rs6754222	0.81[CHB][hapmap]
rs72933220	1.00[ASN][1000 genomes]
rs7572757	1.00[ASN][1000 genomes]
rs7574218	0.82[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7589018	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7598554	0.92[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7606070	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7606220	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap]
rs937726	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10176056	ARID5A	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98916000-98918400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:98916400-98919000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:98917000-98926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:98917200-98918400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:98917200-98924400	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links