Variant report

Variant	rs9650649
Chromosome Location	chr8:10121022-10121023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10120963..10123282-chr8:10135840..10137757,2	K562	blood:
2	chr8:10118764..10122817-chr8:10126495..10130448,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10102621	0.81[TSI][hapmap]
rs10903325	0.87[CEU][hapmap]
rs11249985	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11249990	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11249991	0.87[CEU][hapmap]
rs11774051	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11777018	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11778030	0.82[EUR][1000 genomes]
rs11778901	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs11781529	0.81[EUR][1000 genomes]
rs11782293	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11783091	0.91[CEU][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11783281	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11785954	0.83[EUR][1000 genomes]
rs13257313	1.00[GIH][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs13258691	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13264133	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13269741	0.82[AMR][1000 genomes]
rs13272537	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17695316	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2004677	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2004679	0.96[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34514972	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34917779	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35287467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35524676	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4288377	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4570161	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4840478	0.83[AMR][1000 genomes]
rs4840479	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4841308	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4841315	0.83[AMR][1000 genomes]
rs4841325	0.82[EUR][1000 genomes]
rs4841326	1.00[ASW][hapmap];0.85[GIH][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs55965226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56064712	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6601436	0.82[AMR][1000 genomes]
rs6601438	1.00[GIH][hapmap];0.82[AMR][1000 genomes]
rs71516564	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs723609	0.82[AMR][1000 genomes]
rs7838059	0.82[AMR][1000 genomes]
rs9650648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	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
2	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
3	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
4	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
5	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1028650	chr8:10101815-10178537	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9650649	XKR6	cis	cerebellum	SCAN
rs9650649	PRSS55	cis	cerebellum	SCAN
rs9650649	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10096000-10128000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr8:10103600-10122600	Weak transcription	Spleen	Spleen
3	chr8:10104000-10124600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:10105600-10122800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:10112200-10124600	Weak transcription	Adipose Nuclei	Adipose
6	chr8:10112200-10124600	Weak transcription	Brain Substantia Nigra	brain
7	chr8:10112200-10127800	Weak transcription	Brain Hippocampus Middle	brain
8	chr8:10113000-10123200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:10113600-10124600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:10115400-10122400	Weak transcription	Liver	Liver
11	chr8:10116200-10124600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr8:10118000-10123800	Weak transcription	Brain Germinal Matrix	brain
13	chr8:10118200-10122800	Weak transcription	Pancreas	Pancrea
14	chr8:10118200-10123600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr8:10118200-10127800	Weak transcription	Brain Angular Gyrus	brain
16	chr8:10118200-10128000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr8:10120000-10122000	Weak transcription	Fetal Intestine Large	intestine
18	chr8:10120000-10124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:10120600-10122000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:10120600-10122000	Weak transcription	Fetal Intestine Small	intestine
21	chr8:10120600-10122800	Weak transcription	Colon Smooth Muscle	Colon

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