Variant report

Variant	rs10509681
Chromosome Location	chr10:96798749-96798750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs11188124	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188153	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572082	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572107	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572142	1.00[ASW][hapmap]
rs11572150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11591385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592225	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11593816	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11596254	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11596290	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11596296	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11596943	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11598823	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599203	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11599738	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12761315	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12762602	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12762652	1.00[ASN][1000 genomes]
rs12763201	0.90[CEU][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12763939	1.00[ASN][1000 genomes]
rs12774244	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12777852	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs12779339	1.00[ASN][1000 genomes]
rs12780333	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17442862	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17443251	1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17452671	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs17452714	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs17453533	1.00[ASN][1000 genomes]
rs17523627	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17524348	0.80[CEU][hapmap];1.00[ASN][1000 genomes]
rs17525659	1.00[ASN][1000 genomes]
rs1799853	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1934954	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1934966	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153629	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2185570	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860968	1.00[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34119978	1.00[ASN][1000 genomes]
rs34246390	1.00[ASN][1000 genomes]
rs34254643	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34320910	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34462937	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34883883	1.00[ASN][1000 genomes]
rs34949438	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35203700	1.00[ASN][1000 genomes]
rs35238981	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35461306	1.00[ASN][1000 genomes]
rs35883122	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35955220	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35998772	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36037322	1.00[ASN][1000 genomes]
rs36042065	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36168663	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3980257	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41291560	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4351748	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45523137	1.00[ASN][1000 genomes]
rs45535939	1.00[ASN][1000 genomes]
rs45601238	1.00[ASN][1000 genomes]
rs4607998	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483239	1.00[ASN][1000 genomes]
rs4917636	1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4918704	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4918705	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4918710	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4918716	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4918746	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4918795	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507728	1.00[ASN][1000 genomes]
rs55727865	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55753924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55777838	0.88[AMR][1000 genomes]
rs55804705	0.95[AMR][1000 genomes]
rs56028148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044736	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56090603	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56380192	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56386142	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56408997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570849	1.00[ASN][1000 genomes]
rs595924	1.00[ASN][1000 genomes]
rs601746	1.00[ASN][1000 genomes]
rs61886257	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61886771	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61886773	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61886796	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61886797	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61886802	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888362	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888394	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888396	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888402	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888408	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888409	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888410	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61888411	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs623544	1.00[ASN][1000 genomes]
rs639937	1.00[ASN][1000 genomes]
rs659309	1.00[ASN][1000 genomes]
rs66648066	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs66816038	1.00[ASN][1000 genomes]
rs670565	1.00[ASN][1000 genomes]
rs67728892	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67737822	1.00[ASN][1000 genomes]
rs67851687	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67918795	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs682349	1.00[ASN][1000 genomes]
rs684203	1.00[ASN][1000 genomes]
rs686705	1.00[ASN][1000 genomes]
rs701889	1.00[ASN][1000 genomes]
rs7082506	1.00[ASN][1000 genomes]
rs71482344	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72816690	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72816698	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72816700	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72816701	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72818612	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72818618	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72818642	0.91[AMR][1000 genomes]
rs72818651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818673	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72818681	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72820645	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9332100	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332101	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332102	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332119	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332155	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332163	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332179	1.00[ASN][1000 genomes]
rs9332216	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332222	1.00[MEX][hapmap];0.82[TSI][hapmap];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332238	0.85[MKK][hapmap]
rs9332242	1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1035409	chr10:96495177-96832057	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1050544	chr10:96766934-96814689	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1044182	chr10:96783996-96814689	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv2761618	chr10:96784008-96814689	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10509681	CCNJ	cis	cerebellum	SCAN
rs10509681	HELLS	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96796400-96805400	Strong transcription	Liver	Liver
2	chr10:96797600-96800400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:96798200-96799600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr10:96798400-96799400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links