Variant report

Variant	rs17726209
Chromosome Location	chr8:11022185-11022186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10087767	1.00[CHB][hapmap]
rs10088853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10089518	1.00[CHB][hapmap]
rs10095003	1.00[ASN][1000 genomes]
rs10100660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10101329	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106914	0.81[TSI][hapmap]
rs10110684	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10503415	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs10503416	0.81[TSI][hapmap]
rs10503417	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10903337	1.00[CHB][hapmap]
rs11775489	1.00[ASN][1000 genomes]
rs11776603	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777355	1.00[ASN][1000 genomes]
rs11777887	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs11777918	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs11778121	1.00[CHB][hapmap]
rs11783045	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11783890	1.00[ASN][1000 genomes]
rs11785237	1.00[ASN][1000 genomes]
rs11785392	1.00[CHB][hapmap]
rs11989369	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13248014	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13248264	1.00[CHB][hapmap]
rs13248300	1.00[CHB][hapmap]
rs13249916	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13251528	1.00[CHB][hapmap]
rs13256743	1.00[CHB][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13265553	1.00[CHB][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266785	0.87[CEU][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273857	1.00[CHB][hapmap]
rs13276708	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13276836	1.00[CHB][hapmap]
rs13281566	0.87[EUR][1000 genomes]
rs17152841	1.00[CHB][hapmap]
rs17725480	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17725534	1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17779791	1.00[CHB][hapmap]
rs17782536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782554	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987190	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2409691	1.00[CHB][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409693	1.00[CHB][hapmap]
rs2409695	1.00[CHB][hapmap]
rs2409712	0.82[TSI][hapmap]
rs2409719	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409720	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs2409725	1.00[ASN][1000 genomes]
rs2409726	1.00[ASN][1000 genomes]
rs2409729	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3021495	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021497	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021498	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021501	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34309263	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34367737	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35211404	1.00[ASN][1000 genomes]
rs4291231	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412337	1.00[ASN][1000 genomes]
rs4451268	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs4618656	1.00[CHB][hapmap]
rs4642600	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840548	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841486	1.00[CHB][hapmap]
rs4841497	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841499	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601561	1.00[CHB][hapmap]
rs6601563	1.00[CHB][hapmap]
rs67418928	1.00[ASN][1000 genomes]
rs67559300	1.00[ASN][1000 genomes]
rs71518512	1.00[ASN][1000 genomes]
rs73198943	1.00[ASN][1000 genomes]
rs7830569	0.82[EUR][1000 genomes]
rs7832722	1.00[CHB][hapmap]
rs9329238	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9657544	1.00[CHB][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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv1815171	chr8:10940039-11128712	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1025426	chr8:10942929-11037903	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1026331	chr8:10955941-11046394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv519941	chr8:11016889-11039816	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17726209	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs17726209	AF131215.2	cis	Nerve Tibial	GTEx
rs17726209	FLJ10661	cis	cerebellum	SCAN
rs17726209	TDH	cis	cerebellum	SCAN
rs17726209	CLDN23	cis	multi-tissue	Pritchard
rs17726209	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:11006800-11026200	Weak transcription	HSMM	muscle
3	chr8:11009200-11024800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:11012000-11022400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:11013400-11026400	Weak transcription	Esophagus	oesophagus
6	chr8:11013600-11028800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr8:11015600-11022400	Enhancers	Primary B cells from peripheral blood	blood
8	chr8:11016600-11032200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:11017400-11025400	Weak transcription	HSMMtube	muscle
10	chr8:11020200-11023400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr8:11021000-11022400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:11021000-11022400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr8:11021000-11022600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr8:11021000-11022600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr8:11021200-11022400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr8:11021200-11022600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr8:11021200-11023000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr8:11021400-11022400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:11021400-11022600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr8:11021400-11022600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr8:11021400-11022600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr8:11021400-11023000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr8:11021800-11024800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr8:11021800-11025000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:11021800-11026200	Weak transcription	Pancreas	Pancrea
26	chr8:11021800-11026400	Weak transcription	Gastric	stomach
27	chr8:11022000-11022200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:11022000-11022200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr8:11022000-11022400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr8:11022000-11022600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr8:11022000-11022600	Enhancers	GM12878-XiMat	blood
32	chr8:11022000-11025600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr8:11022000-11026000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr8:11022000-11026400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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