Variant report

Variant	rs17748464
Chromosome Location	chr8:10050618-10050619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10085917	0.81[CEU][hapmap]
rs10093457	0.81[EUR][1000 genomes]
rs10097315	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs10104463	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10283047	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11249973	0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11774836	0.82[CHD][hapmap]
rs11783143	0.83[CHD][hapmap]
rs11786117	0.86[MEX][hapmap]
rs11993663	0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs12548428	0.82[CHD][hapmap];0.82[MEX][hapmap]
rs13257383	0.87[CHD][hapmap]
rs1484646	0.81[CHD][hapmap]
rs1484647	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1484648	0.92[CEU][hapmap]
rs1905630	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs1905631	0.88[CEU][hapmap]
rs1905633	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1905634	0.92[CEU][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2409623	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28701812	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4448276	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56883717	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60032918	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60498378	0.83[AMR][1000 genomes]
rs6601419	0.88[JPT][hapmap]
rs6601420	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6982806	0.96[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6997464	0.85[CEU][hapmap];0.84[CHD][hapmap];0.87[MEX][hapmap]
rs7006628	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]
rs7011004	0.80[CEU][hapmap]
rs7011281	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs7011821	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs7812517	0.81[CEU][hapmap];0.81[CHD][hapmap]
rs7820236	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7822181	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7829478	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7842065	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7845503	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17748464	XKR5	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10048200-10052200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:10049000-10051200	Enhancers	Fetal Brain Male	brain
3	chr8:10049400-10050800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:10049400-10051000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:10049600-10051000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:10049800-10050800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:10049800-10050800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr8:10050000-10051000	Enhancers	Fetal Brain Female	brain
9	chr8:10050000-10057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr8:10050000-10068000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:10050200-10053600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr8:10050400-10054600	Weak transcription	HMEC	breast
13	chr8:10050400-10054600	Weak transcription	NHEK	skin
14	chr8:10050400-10055000	Weak transcription	HSMMtube	muscle
15	chr8:10050400-10058000	Weak transcription	Aorta	Aorta
16	chr8:10050600-10050800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr8:10050600-10054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:10050600-10055000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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