Variant report

Variant	rs2409691
Chromosome Location	chr8:10943276-10943277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10087767	1.00[CHB][hapmap]
rs10088853	1.00[CHB][hapmap]
rs10089518	1.00[CHB][hapmap];0.95[MEX][hapmap]
rs10100660	1.00[CHB][hapmap]
rs10101329	1.00[CHB][hapmap]
rs10105315	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10106207	0.84[CEU][hapmap]
rs10108304	1.00[CHD][hapmap]
rs10108618	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10110684	1.00[CHB][hapmap]
rs10113808	0.96[CEU][hapmap]
rs10503417	1.00[CHB][hapmap]
rs10903337	1.00[CHB][hapmap]
rs11250092	1.00[CHB][hapmap]
rs11773990	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11776603	1.00[CHB][hapmap]
rs11777887	1.00[CHB][hapmap]
rs11777918	1.00[CHB][hapmap]
rs11778121	1.00[CHB][hapmap]
rs11783045	1.00[CHB][hapmap]
rs11785392	1.00[CHB][hapmap]
rs11986748	1.00[CHD][hapmap]
rs11989369	1.00[CHB][hapmap]
rs11991118	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11991121	1.00[CHD][hapmap]
rs11991716	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12546366	0.81[MEX][hapmap]
rs13248014	1.00[CHB][hapmap]
rs13248264	1.00[CHB][hapmap]
rs13248300	1.00[CHB][hapmap]
rs13249916	1.00[CHB][hapmap]
rs13251528	1.00[CHB][hapmap]
rs13256743	1.00[CHB][hapmap]
rs13265553	1.00[CHB][hapmap]
rs13273857	1.00[CHB][hapmap]
rs13276708	1.00[CHB][hapmap]
rs13276836	1.00[CHB][hapmap]
rs17152841	1.00[CHB][hapmap]
rs17723229	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17724467	0.85[CEU][hapmap]
rs17725480	1.00[CHB][hapmap]
rs17725534	1.00[CHB][hapmap]
rs17726209	1.00[CHB][hapmap]
rs17779791	1.00[CHB][hapmap]
rs17782536	1.00[CHB][hapmap]
rs17782554	1.00[CHB][hapmap]
rs1987190	1.00[CHB][hapmap]
rs2001329	0.81[CEU][hapmap]
rs2001433	0.89[CEU][hapmap]
rs2409689	0.85[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2409692	1.00[CHB][hapmap]
rs2409693	1.00[CHB][hapmap]
rs2409694	0.83[ASW][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs2409695	1.00[CHB][hapmap]
rs2409718	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs2409719	1.00[CHB][hapmap]
rs2409720	1.00[CHB][hapmap]
rs2409729	1.00[CHB][hapmap]
rs28722721	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2898256	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2898257	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2898260	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2898261	0.80[MEX][hapmap]
rs3021494	0.90[MEX][hapmap]
rs3021495	1.00[CHB][hapmap]
rs3021497	1.00[CHB][hapmap]
rs3021500	0.81[CEU][hapmap]
rs34094119	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4240671	1.00[CHB][hapmap];0.81[MEX][hapmap]
rs4240672	1.00[CHB][hapmap]
rs4291231	1.00[CHB][hapmap]
rs4326350	1.00[CHB][hapmap]
rs4451268	1.00[CHB][hapmap]
rs4523214	0.92[CEU][hapmap]
rs4618656	1.00[CHB][hapmap]
rs4642600	1.00[CHB][hapmap]
rs4840542	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4840548	1.00[CHB][hapmap]
rs4841460	1.00[CHB][hapmap]
rs4841465	0.82[CEU][hapmap]
rs4841486	1.00[CHB][hapmap]
rs4841489	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4841490	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4841495	1.00[CEU][hapmap]
rs4841497	1.00[CHB][hapmap]
rs4841498	0.90[MEX][hapmap]
rs4841504	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs6601559	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6601560	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6601561	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs6601562	0.92[CEU][hapmap]
rs6601563	1.00[CHB][hapmap]
rs6601564	0.95[MEX][hapmap]
rs6980856	0.85[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6982381	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6985109	1.00[CHB][hapmap]
rs6991930	0.92[CEU][hapmap]
rs7010590	0.85[MEX][hapmap]
rs7011756	0.81[CEU][hapmap]
rs7017567	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7460507	0.85[MEX][hapmap]
rs7820860	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7821826	1.00[CHB][hapmap]
rs7832722	1.00[CHB][hapmap]
rs7835318	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9329238	1.00[CHB][hapmap]
rs9657519	0.89[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9657544	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2409691	C8orf5	cis	uninvolved skin	skin_eQTL
rs2409691	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2409691	C8orf13	cis	multi-tissue	Pritchard
rs2409691	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10925600-10944400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr8:10935200-10943800	Weak transcription	Brain Anterior Caudate	brain
3	chr8:10940600-10943400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:10942200-10944400	Enhancers	Fetal Heart	heart
5	chr8:10942400-10943400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:10942400-10943400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr8:10942600-10943400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:10942800-10943400	Bivalent Enhancer	Fetal Brain Male	brain
9	chr8:10943000-10948400	Weak transcription	Gastric	stomach

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