Variant report

Variant	rs11778398
Chromosome Location	chr8:10974243-10974244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10087081	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10105315	1.00[CHB][hapmap]
rs10105377	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10108618	1.00[CHB][hapmap]
rs10113808	1.00[CHB][hapmap]
rs10282848	1.00[CHD][hapmap]
rs10503420	1.00[CHD][hapmap]
rs1057625	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11250117	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11773990	1.00[CHB][hapmap]
rs11777887	1.00[CHB][hapmap]
rs11777918	1.00[CHB][hapmap]
rs11991118	1.00[CHB][hapmap]
rs11991716	1.00[CHB][hapmap]
rs17152862	1.00[CHD][hapmap]
rs17152978	1.00[CHD][hapmap]
rs17153088	1.00[CHD][hapmap]
rs17724226	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17780806	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001433	1.00[CHB][hapmap]
rs2409689	1.00[CHB][hapmap]
rs2409692	1.00[CHB][hapmap]
rs2409694	1.00[CHB][hapmap]
rs2409720	1.00[CHB][hapmap]
rs28417109	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2898257	1.00[CHB][hapmap]
rs2898260	1.00[CHB][hapmap]
rs34208825	1.00[ASN][1000 genomes]
rs34772085	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36089015	0.82[EUR][1000 genomes]
rs4840542	1.00[CHB][hapmap]
rs4840551	1.00[CHB][hapmap]
rs4841489	1.00[CHB][hapmap]
rs4841490	1.00[CHB][hapmap]
rs60921132	0.82[EUR][1000 genomes]
rs6601560	1.00[CHB][hapmap]
rs6601562	1.00[CHB][hapmap]
rs6980856	1.00[CHB][hapmap]
rs6981201	0.85[AMR][1000 genomes]
rs6991930	1.00[CHB][hapmap]
rs7460507	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7825690	1.00[CHB][hapmap]
rs9657519	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	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
7	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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11778398	AF131215.2	cis	lung	GTEx
rs11778398	CTSB	cis	cerebellum	SCAN
rs11778398	AF131215.9	cis	lung	GTEx
rs11778398	AF131215.9	cis	Skin Sun Exposed Lower leg	GTEx
rs11778398	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs11778398	AF131215.9	cis	Esophagus Mucosa	GTEx
rs11778398	TDH	cis	cerebellum	SCAN
rs11778398	AF131215.2	cis	Nerve Tibial	GTEx
rs11778398	C8orf5	cis	normal skin	skin_eQTL
rs11778398	AF131215.2	cis	Stomach	GTEx
rs11778398	MFHAS1	cis	cerebellum	SCAN
rs11778398	PRSS55	cis	cerebellum	SCAN
rs11778398	AF131215.9	cis	Heart Left Ventricle	GTEx
rs11778398	TDH	cis	parietal	SCAN
rs11778398	AF131215.2	cis	Esophagus Mucosa	GTEx
rs11778398	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10958400-10974800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr8:10961200-10975400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr8:10963000-10981200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr8:10963600-10974800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr8:10965800-10974400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr8:10965800-10981600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:10966200-10981400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:10967200-10974800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr8:10972000-10975800	Weak transcription	Left Ventricle	heart
12	chr8:10972000-10977400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr8:10973800-10974400	Enhancers	GM12878-XiMat	blood
14	chr8:10974200-10974400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr8:10974200-10974400	Enhancers	Pancreas	Pancrea
16	chr8:10974200-10974600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr8:10974200-10975000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:10974200-10975000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr8:10974200-10975000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr8:10974200-10975600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr8:10974200-10975800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr8:10974200-10975800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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