Variant report

Variant	rs7006628
Chromosome Location	chr8:10045113-10045114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10085917	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10093457	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10097315	0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs10104463	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10283047	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11249973	0.85[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11777161	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11783143	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs11786117	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs11786120	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs11787363	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13257383	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1484648	0.85[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs17151318	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs17748267	0.85[CEU][hapmap]
rs17748464	0.85[CEU][hapmap];0.91[CHD][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1905630	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1905631	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs1905632	0.84[ASN][1000 genomes]
rs1905633	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1905634	0.85[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs2409623	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28380058	0.83[EUR][1000 genomes]
rs28448513	0.85[ASN][1000 genomes]
rs28701812	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2898240	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3958939	0.83[ASN][1000 genomes]
rs4255142	0.82[JPT][hapmap]
rs4448276	0.92[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59255182	0.83[AMR][1000 genomes]
rs60032918	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60498378	0.86[AMR][1000 genomes]
rs6601420	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6981758	0.85[JPT][hapmap]
rs6982806	0.88[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6994636	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6996281	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6997464	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7011004	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7011281	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7011821	0.96[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs7812517	0.86[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs7820236	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7822181	0.86[ASN][1000 genomes]
rs7829478	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7842065	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7845503	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv890344	chr8:9995515-10060638	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1026335	chr8:10037279-10139782	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv516061	chr8:10045113-10045451	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7006628	XKR5	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10042800-10049400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:10043400-10046600	Enhancers	Fetal Brain Male	brain
3	chr8:10043800-10046400	Weak transcription	Aorta	Aorta
4	chr8:10044200-10050000	Weak transcription	Fetal Brain Female	brain
5	chr8:10044400-10048000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr8:10044800-10045800	Enhancers	Primary hematopoietic stem cells	blood
7	chr8:10045000-10045600	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links