Variant report

Variant	rs40899
Chromosome Location	chr7:108169262-108169263
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	FOSL1	chr7:108168626-108169330	HCT-116	colon:	n/a	n/a
2	FOS	chr7:108168680-108169439	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr7:108168592-108169356	HCT-116	colon:	n/a	n/a
4	NFIC	chr7:108168611-108169334	ECC-1	luminal epithelium:	n/a	n/a
5	E2F4	chr7:108168750-108169320	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr7:108168588-108169328	HCT-116	colon:	n/a	n/a
7	SP1	chr7:108168533-108169352	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
2	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:
3	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:

Variant related genes	Relation type
PNPLA8	TF binding region
ENSG00000128590	Chromatin interaction
ENSG00000177683	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10487859	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973105	0.84[EUR][1000 genomes]
rs11974559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976021	0.80[MEX][hapmap]
rs11981670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12666562	0.86[ASN][1000 genomes]
rs12705470	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs13227836	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs13228190	0.83[EUR][1000 genomes]
rs13229488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238841	0.89[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs13245101	0.84[EUR][1000 genomes]
rs13245242	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs13307045	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13312593	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17155828	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17338441	0.84[EUR][1000 genomes]
rs17338462	0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs17423043	0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs17423119	0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs17424206	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194587	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214913	0.84[EUR][1000 genomes]
rs2214914	0.88[EUR][1000 genomes]
rs2214915	0.89[EUR][1000 genomes]
rs2300048	0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2300052	0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs3202837	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33987381	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34218460	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.91[EUR][1000 genomes]
rs34814097	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34887057	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35372181	0.88[ASN][1000 genomes]
rs35436957	0.83[EUR][1000 genomes]
rs35617326	0.84[EUR][1000 genomes]
rs35880371	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763457	0.83[ASN][1000 genomes]
rs40843	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40850	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40854	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40875	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40880	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40882	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40885	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40895	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40901	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40902	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40915	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40921	0.84[ASN][1000 genomes]
rs40923	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40924	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40925	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40928	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40934	0.86[ASN][1000 genomes]
rs40938	0.86[ASN][1000 genomes]
rs40939	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40940	0.86[ASN][1000 genomes]
rs40941	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40944	0.86[ASN][1000 genomes]
rs40945	0.86[ASN][1000 genomes]
rs40946	0.86[ASN][1000 genomes]
rs40947	1.00[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs41385644	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4992578	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.81[EUR][1000 genomes]
rs59458537	0.82[EUR][1000 genomes]
rs60398019	0.81[EUR][1000 genomes]
rs60426977	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466233	0.83[EUR][1000 genomes]
rs6466238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461825	0.84[EUR][1000 genomes]
rs67027479	0.84[EUR][1000 genomes]
rs67694466	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6947492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949637	0.84[EUR][1000 genomes]
rs6955152	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959023	0.83[EUR][1000 genomes]
rs6967368	0.91[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6976309	0.84[EUR][1000 genomes]
rs6976649	0.83[EUR][1000 genomes]
rs6976659	0.84[EUR][1000 genomes]
rs6976752	0.84[EUR][1000 genomes]
rs6976776	0.84[EUR][1000 genomes]
rs6976804	0.84[EUR][1000 genomes]
rs6978552	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs71213282	0.84[EUR][1000 genomes]
rs71568528	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs7786947	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7790875	0.89[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7806869	0.82[EUR][1000 genomes]
rs7807737	0.84[EUR][1000 genomes]
rs7807941	0.84[EUR][1000 genomes]
rs7811808	0.85[EUR][1000 genomes]
rs9649307	0.84[EUR][1000 genomes]
rs9649308	0.85[EUR][1000 genomes]
rs9785056	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs40899	THAP5	cis	lymphoblastoid	seeQTL
rs40899	THAP5	cis	multi-tissue	Pritchard
rs40899	THAP5	cis	normal skin	skin_eQTL
rs40899	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40899	THAP5	cis	Esophagus Muscularis	GTEx
rs40899	C7orf66	cis	cerebellum	SCAN
rs40899	THAP5	cis	Muscle Skeletal	GTEx
rs40899	PRKAR2B	cis	parietal	SCAN
rs40899	THAP5	cis	Heart Left Ventricle	GTEx
rs40899	THAP5	cis	uninvolved skin	skin_eQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108167200-108170000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:108167400-108173400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:108167600-108170000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:108167600-108170000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:108167600-108176200	Weak transcription	Primary B cells from cord blood	blood
6	chr7:108167800-108169600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:108167800-108169600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:108167800-108170400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:108168800-108169800	Weak transcription	HMEC	breast
10	chr7:108168800-108170000	Weak transcription	Placenta	Placenta
11	chr7:108168800-108175800	Weak transcription	K562	blood
12	chr7:108169000-108170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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