Variant report

Variant	rs10258848
Chromosome Location	chr7:146344105-146344106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10234219	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10277654	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10280592	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10487927	0.81[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap]
rs10952646	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs10952648	0.88[JPT][hapmap]
rs1155384	0.82[ASW][hapmap];0.92[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12703821	0.81[TSI][hapmap]
rs13222136	0.81[TSI][hapmap]
rs13227381	0.81[TSI][hapmap]
rs13239405	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13239605	0.81[JPT][hapmap]
rs13247654	1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1494450	0.90[JPT][hapmap]
rs1494455	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17513926	0.82[MEX][hapmap]
rs17517293	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs17586018	0.81[TSI][hapmap]
rs1908320	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs347180	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs347195	0.84[CEU][hapmap]
rs347198	0.85[CEU][hapmap]
rs347201	0.85[CEU][hapmap]
rs347202	0.85[CEU][hapmap]
rs347204	0.85[CEU][hapmap]
rs347205	0.85[CEU][hapmap]
rs347206	0.85[CEU][hapmap]
rs347209	0.85[CEU][hapmap]
rs347211	0.85[CEU][hapmap]
rs347212	0.85[CEU][hapmap]
rs347215	0.85[CEU][hapmap]
rs347216	0.85[CEU][hapmap]
rs347217	0.85[CEU][hapmap]
rs347220	0.81[CHD][hapmap]
rs347222	0.85[CEU][hapmap]
rs347223	0.90[JPT][hapmap]
rs369723	0.90[JPT][hapmap]
rs445561	0.90[JPT][hapmap]
rs4726808	0.85[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4726809	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6957488	0.90[JPT][hapmap]
rs714584	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs724216	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7456508	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7458498	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7458540	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7789802	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7810281	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9691874	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs9886307	1.00[CEU][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889391	chr7:146168418-146389259	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1032959	chr7:146193191-146351005	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1021967	chr7:146199590-146413808	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1015996	chr7:146202073-146419347	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv934014	chr7:146212698-146400508	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1022547	chr7:146226298-146624409	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv996300	chr7:146236230-146663300	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1025948	chr7:146252115-146393151	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv948895	chr7:146260214-146348562	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1018605	chr7:146287876-146448400	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv889392	chr7:146292088-146446767	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1027561	chr7:146308783-146762872	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv1034346	chr7:146326815-146367793	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv608939	chr7:146332953-146464965	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv526330	chr7:146342322-146371181	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv2761378	chr7:146343685-146344283	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
17	nsv1021923	chr7:146344105-146442062	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv1021542	chr7:146344105-146564397	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10258848	EPHB6	cis	parietal	SCAN
rs10258848	OR2A2	cis	parietal	SCAN
rs10258848	TPK1	cis	cerebellum	SCAN
rs10258848	ZNF398	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:146342400-146345400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:146342600-146345200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:146343400-146348800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:146343600-146345200	Enhancers	Fetal Thymus	thymus
5	chr7:146344000-146344200	Enhancers	Pancreas	Pancrea

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