Variant report

Variant	rs7902245
Chromosome Location	chr10:26956495-26956496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:26955921..26958837-chr10:26961876..26965160,3	K562	blood:
2	chr10:26953025..26955897-chr10:26956336..26959208,3	K562	blood:
3	chr10:26948657..26951534-chr10:26954538..26957242,4	K562	blood:

Variant related genes	Relation type
ENSG00000227932	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10741117	1.00[YRI][hapmap]
rs10829047	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10829048	0.90[EUR][1000 genomes]
rs11015209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11015211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11015212	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11015216	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11015218	0.91[EUR][1000 genomes]
rs12246285	0.83[EUR][1000 genomes]
rs12260298	0.88[EUR][1000 genomes]
rs12260466	0.83[EUR][1000 genomes]
rs12761447	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17747622	1.00[CHB][hapmap]
rs1998632	1.00[YRI][hapmap]
rs34691042	0.82[EUR][1000 genomes]
rs34814552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34901510	0.89[EUR][1000 genomes]
rs35534478	0.89[EUR][1000 genomes]
rs35687107	0.88[EUR][1000 genomes]
rs35827769	0.89[EUR][1000 genomes]
rs35841691	0.91[EUR][1000 genomes]
rs36006550	0.89[EUR][1000 genomes]
rs61841662	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7896300	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7905561	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3436664	chr10:26860755-26969397	Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv894977	chr10:26876272-26959202	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1044848	chr10:26890410-26961634	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1052412	chr10:26890945-26961634	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1041766	chr10:26890945-26969381	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1046911	chr10:26894348-26969381	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1044057	chr10:26894348-26971879	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv516275	chr10:26896432-26968171	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3333006	chr10:26908323-26985227	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3353004	chr10:26912762-26966282	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv947778	chr10:26944706-26958639	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7902245	TPRT	cis	multi-tissue	Pritchard
rs7902245	SOX18	trans	lymphoblastoid	seeQTL
rs7902245	ABI1	cis	cerebellum	SCAN
rs7902245	LOC387646	cis	cerebellum	SCAN
rs7902245	LYZL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26956000-26957000	Strong transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links