Variant report

Variant	rs7460507
Chromosome Location	chr8:10969075-10969076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10087081	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10105377	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10106207	1.00[JPT][hapmap]
rs10503415	1.00[JPT][hapmap]
rs1057625	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11250117	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11250119	0.82[JPT][hapmap]
rs11778121	0.83[EUR][1000 genomes]
rs11778398	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11991118	0.85[MEX][hapmap]
rs17724226	1.00[CEU][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17724467	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17780806	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2409689	0.85[MEX][hapmap]
rs2409691	0.85[MEX][hapmap]
rs2409710	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2409713	0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2409714	0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2409715	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2409716	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2409717	0.83[ASN][1000 genomes]
rs2409718	0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs28417109	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28630509	0.81[ASN][1000 genomes]
rs2898261	0.95[MEX][hapmap]
rs3021494	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs3021500	1.00[JPT][hapmap]
rs34772085	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4333549	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4523214	0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4618656	0.80[EUR][1000 genomes]
rs4840544	0.89[ASN][1000 genomes]
rs4840549	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4841495	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4841501	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs60921132	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601563	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6601564	1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs6980856	0.85[MEX][hapmap]
rs6981201	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6981352	0.81[EUR][1000 genomes]
rs6995204	0.85[ASN][1000 genomes]
rs6996752	0.88[CHD][hapmap]
rs6996846	0.91[ASN][1000 genomes]
rs7004825	0.82[JPT][hapmap]
rs7005680	0.82[ASN][1000 genomes]
rs7010590	0.88[CHD][hapmap]
rs7011756	1.00[JPT][hapmap]
rs7823349	1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7829396	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7832722	0.84[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1027845	chr8:10959666-10995565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7460507	AF131215.2	cis	Nerve Tibial	GTEx
rs7460507	AF131215.2	cis	Stomach	GTEx
rs7460507	FLJ10661	cis	cerebellum	SCAN
rs7460507	TDH	cis	parietal	SCAN
rs7460507	CTSB	cis	cerebellum	SCAN
rs7460507	AF131215.9	cis	Heart Left Ventricle	GTEx
rs7460507	PRSS55	cis	cerebellum	SCAN
rs7460507	AF131215.9	cis	Skin Sun Exposed Lower leg	GTEx
rs7460507	MFHAS1	cis	cerebellum	SCAN
rs7460507	TDH	cis	cerebellum	SCAN
rs7460507	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs7460507	CLDN23	cis	multi-tissue	Pritchard
rs7460507	AF131215.2	cis	Esophagus Mucosa	GTEx
rs7460507	AF131215.9	cis	Esophagus Mucosa	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10958200-10970200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:10958400-10974800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr8:10958600-10971200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr8:10958600-10971200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr8:10960800-10970800	Weak transcription	HSMM	muscle
6	chr8:10961200-10975400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr8:10961600-10970600	Weak transcription	Fetal Intestine Large	intestine
8	chr8:10961800-10971400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr8:10962400-10969600	Weak transcription	NH-A	brain
10	chr8:10963000-10981200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr8:10963200-10970400	Weak transcription	Primary B cells from cord blood	blood
12	chr8:10963400-10971400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:10963600-10971200	Weak transcription	HSMMtube	muscle
14	chr8:10963600-10973600	Weak transcription	Lung	lung
15	chr8:10963600-10974800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr8:10964200-10971400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr8:10965400-10971400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr8:10965600-10970800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:10965600-10973600	Weak transcription	Esophagus	oesophagus
20	chr8:10965600-10974200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:10965800-10970800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr8:10965800-10971400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr8:10965800-10974400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr8:10965800-10981600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr8:10966200-10970200	Weak transcription	Fetal Intestine Small	intestine
26	chr8:10966200-10972000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:10966200-10981400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr8:10966400-10974200	Weak transcription	Pancreas	Pancrea
30	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:10966600-10974200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr8:10966800-10971400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:10966800-10972000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr8:10967200-10974800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr8:10968000-10972600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr8:10968200-10970800	Weak transcription	GM12878-XiMat	blood
37	chr8:10968800-10969200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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