Variant report

Variant	rs6601578
Chromosome Location	chr8:11136604-11136605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11136381..11138935-chr8:11140038..11142667,3	K562	blood:

Variant related genes	Relation type
ENSG00000104643	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10096194	0.92[YRI][hapmap]
rs10098322	1.00[ASW][hapmap];0.82[CHD][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap]
rs10098488	0.92[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes]
rs10099569	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10104728	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10107010	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10110557	0.92[YRI][hapmap]
rs10503418	0.85[CEU][hapmap]
rs11250127	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11250129	0.83[MEX][hapmap]
rs11775635	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13253735	0.91[LWK][hapmap];0.92[YRI][hapmap]
rs13270679	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13279067	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1347410	0.80[CEU][hapmap]
rs1435278	0.82[EUR][1000 genomes]
rs17797443	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1897950	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1897951	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2060459	0.86[YRI][hapmap]
rs2060465	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2099456	0.96[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs2164272	0.81[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2164273	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2293855	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2293856	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2572397	0.81[CEU][hapmap]
rs2572398	0.80[CEU][hapmap]
rs2572417	0.81[CEU][hapmap]
rs2572418	0.81[CEU][hapmap]
rs2572419	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2736277	0.92[CEU][hapmap]
rs28507159	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35392635	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3779891	1.00[ASW][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs3808509	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3808513	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3808518	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808519	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4559208	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4568582	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4840554	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6601579	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6984759	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6985146	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs6985460	0.81[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6991074	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6991606	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6995404	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs7003241	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7004362	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7005469	1.00[YRI][hapmap]
rs7016671	1.00[ASW][hapmap];0.81[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs718427	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs765731	0.81[EUR][1000 genomes]
rs7837036	0.83[EUR][1000 genomes]
rs7838897	1.00[YRI][hapmap]
rs7839053	0.91[YRI][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	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
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6601578	C8orf48	cis	cerebellum	SCAN
rs6601578	THEX1	Cis_chr	lymphoblastoid	RTeQTL
rs6601578	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs6601578	PRSS55	cis	cerebellum	SCAN
rs6601578	TDH	cis	parietal	SCAN
rs6601578	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs6601578	FLJ10661	cis	cerebellum	SCAN
rs6601578	DEFB134	cis	cerebellum	SCAN
rs6601578	TDH	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11135600-11141200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr8:11136000-11141000	Weak transcription	Colon Smooth Muscle	Colon

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