Variant report

Variant	rs3808603
Chromosome Location	chr8:10698218-10698219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:10696371-10698275	PBDE	blood:	n/a	n/a
2	MXI1	chr8:10696164-10698606	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr8:10696084-10698426	GM12891	blood:	n/a	n/a
4	POLR2A	chr8:10696212-10698336	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:10687156..10690707-chr8:10693616..10698468,7	K562	blood:
2	chr8:10690421..10694581-chr8:10695821..10698975,5	MCF-7	breast:
3	chr8:10528112..10530692-chr8:10696880..10699073,2	K562	blood:

Variant related genes	Relation type
PINX1	TF binding region
ENSG00000258724	TF binding region
SOX7	TF binding region
ENSG00000171060	Chromatin interaction
ENSG00000254093	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10046628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs10089153	0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs10091386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10093774	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs10098699	0.84[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10099929	0.95[ASN][1000 genomes]
rs10109416	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10109550	0.87[CHB][hapmap]
rs10481451	0.84[CEU][hapmap]
rs11250077	0.84[CEU][hapmap]
rs11250081	0.95[ASN][1000 genomes]
rs11250083	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs11776674	0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11776767	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11986013	0.81[ASN][1000 genomes]
rs11986015	0.81[ASN][1000 genomes]
rs11986043	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11986845	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11986935	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11996727	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12541110	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12542888	0.80[CEU][hapmap]
rs12676417	0.84[CEU][hapmap]
rs13254059	0.90[ASN][1000 genomes]
rs13254592	0.90[ASN][1000 genomes]
rs13274017	0.89[ASN][1000 genomes]
rs1469556	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs1469557	0.80[CHD][hapmap]
rs1549796	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17152576	0.89[ASN][1000 genomes]
rs1991649	0.91[ASN][1000 genomes]
rs1991650	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1991651	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2271355	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2271357	0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2277130	0.84[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2278335	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2292370	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2292371	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2409649	0.91[ASN][1000 genomes]
rs2409650	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2409676	0.81[JPT][hapmap]
rs28613656	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34653170	0.84[ASN][1000 genomes]
rs35091929	0.95[ASN][1000 genomes]
rs3808605	0.83[ASN][1000 genomes]
rs4840516	0.80[CEU][hapmap]
rs4840519	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4841452	0.86[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs6601529	0.84[CEU][hapmap];0.81[GIH][hapmap]
rs6601533	0.90[ASN][1000 genomes]
rs6601534	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601535	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601536	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66844016	0.91[ASN][1000 genomes]
rs67211633	0.89[ASN][1000 genomes]
rs6980805	0.84[CEU][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs6982769	0.91[ASN][1000 genomes]
rs6984388	0.91[ASN][1000 genomes]
rs6987200	0.91[ASN][1000 genomes]
rs6988598	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6989160	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs6989846	0.87[CHB][hapmap]
rs6990055	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6990589	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs6991499	0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6991526	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6992366	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6993121	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7000939	0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7001887	0.95[ASN][1000 genomes]
rs7002282	0.84[CEU][hapmap]
rs7004998	0.94[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7005531	0.81[CHB][hapmap]
rs7010680	0.94[ASN][1000 genomes]
rs7010709	0.87[CHB][hapmap];0.93[CHD][hapmap]
rs7012206	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7013032	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs7814757	0.84[CEU][hapmap]
rs7818181	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7824384	0.87[CHB][hapmap]
rs7825100	0.88[ASN][1000 genomes]
rs7829089	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7829201	0.90[ASN][1000 genomes]
rs7830317	0.98[ASN][1000 genomes]
rs7830431	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7833128	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7833945	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7840785	0.81[CHB][hapmap]
rs7846449	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9969626	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831232	chr8:10606053-10774948	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1019754	chr8:10617908-10700140	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv539471	chr8:10617908-10700140	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1031726	chr8:10627742-10749369	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv508497	chr8:10680621-10750255	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3808603	DEFB136	cis	parietal	SCAN
rs3808603	FLJ10661	cis	cerebellum	SCAN
rs3808603	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs3808603	MFHAS1	cis	cerebellum	SCAN
rs3808603	AMAC1L2	cis	parietal	SCAN
rs3808603	DEFA6	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10698000-10698400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr8:10698000-10698400	Enhancers	HepG2	liver
3	chr8:10698000-10699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:10698000-10702400	Weak transcription	Liver	Liver
5	chr8:10698000-10707800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr8:10698200-10698600	Enhancers	Dnd41	blood
7	chr8:10698200-10699600	Enhancers	HMEC	breast
8	chr8:10698200-10699800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:10698200-10699800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:10698200-10699800	Enhancers	NHEK	skin
11	chr8:10698200-10700600	Weak transcription	GM12878-XiMat	blood

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