Variant report

Variant	rs4841498
Chromosome Location	chr8:10985432-10985433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10087081	1.00[CHB][hapmap]
rs10089518	0.85[MEX][hapmap]
rs10105315	0.81[CEU][hapmap]
rs10106207	0.84[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs10106914	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10108618	0.85[MEX][hapmap]
rs10113808	0.81[CEU][hapmap]
rs10503416	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11250119	1.00[CHB][hapmap]
rs11773990	0.85[CEU][hapmap]
rs11984987	1.00[JPT][hapmap]
rs11986294	1.00[JPT][hapmap]
rs11991118	0.81[CEU][hapmap];0.90[MEX][hapmap]
rs13276836	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17724467	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17783634	1.00[CHB][hapmap]
rs2001328	0.96[ASN][1000 genomes]
rs2001329	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001433	0.88[CEU][hapmap]
rs2409689	0.85[CEU][hapmap];0.90[MEX][hapmap]
rs2409691	0.90[MEX][hapmap]
rs2409710	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2409712	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2409713	0.82[CHB][hapmap]
rs2409714	0.82[CHB][hapmap]
rs2409715	0.82[CHB][hapmap]
rs2409716	0.82[CHB][hapmap]
rs2409718	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs2409742	1.00[CHB][hapmap]
rs2898257	0.84[CEU][hapmap]
rs3021494	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs3021500	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs34208825	0.87[EUR][1000 genomes]
rs4333549	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4523214	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4840544	0.85[AMR][1000 genomes]
rs4840549	0.82[CHB][hapmap]
rs4840551	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs4841465	0.81[CEU][hapmap]
rs4841489	0.85[CEU][hapmap]
rs4841490	0.84[CEU][hapmap]
rs4841500	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4841501	0.82[CHB][hapmap]
rs4841503	0.81[EUR][1000 genomes]
rs4841504	0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4841507	0.82[CHB][hapmap]
rs6601560	0.82[CEU][hapmap]
rs6601564	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6651507	1.00[JPT][hapmap]
rs6980856	0.85[CEU][hapmap];0.90[MEX][hapmap]
rs6986032	1.00[CHB][hapmap]
rs6996846	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7004825	0.81[CEU][hapmap]
rs7005680	0.85[EUR][1000 genomes]
rs7010590	1.00[CHB][hapmap]
rs7011756	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7813802	1.00[CHB][hapmap]
rs7819412	0.82[CHB][hapmap]
rs7823349	0.82[CHB][hapmap]
rs7829396	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7843934	1.00[JPT][hapmap]
rs9657519	0.81[CEU][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv1019796	chr8:10979442-11010826	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4841498	C8orf5	cis	normal skin	skin_eQTL
rs4841498	C8orf13	cis	multi-tissue	Pritchard
rs4841498	FLJ10661	cis	cerebellum	SCAN
rs4841498	DEFB134	cis	cerebellum	SCAN
rs4841498	AF131215.9	cis	Esophagus Mucosa	GTEx
rs4841498	PRSS55	cis	cerebellum	SCAN
rs4841498	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs4841498	CLDN23	cis	multi-tissue	Pritchard
rs4841498	CTSB	cis	cerebellum	SCAN
rs4841498	MFHAS1	cis	cerebellum	SCAN
rs4841498	TDH	cis	cerebellum	SCAN
rs4841498	AF131215.2	cis	Stomach	GTEx
rs4841498	AF131215.9	cis	Skin Sun Exposed Lower leg	GTEx
rs4841498	AF131215.9	cis	Heart Left Ventricle	GTEx
rs4841498	FAM167A	cis	lymphoblastoid	seeQTL
rs4841498	TDH	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10966200-10999000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:10966400-11026200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:10982800-10985800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:10982800-11003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr8:10983000-10985800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr8:10983000-11002000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr8:10983000-11003200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr8:10983200-10989400	Weak transcription	Pancreas	Pancrea
9	chr8:10983200-10991000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr8:10983200-10997000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:10983200-11001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:10983400-10985600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr8:10983400-10985800	Weak transcription	Spleen	Spleen
14	chr8:10983400-10990800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr8:10983600-10990600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr8:10983600-10991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr8:10984400-11000000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:10985000-10986000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr8:10985400-10989600	Enhancers	GM12878-XiMat	blood

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