Variant report

Variant	rs40900
Chromosome Location	chr7:108170151-108170152
allele	A/G
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	FOXA1	chr7:108169880-108170179	T-47D	breast:	n/a	n/a
2	POLR2A	chr7:108169704-108170212	H1-neurons	neurons:	n/a	n/a
3	FOXA1	chr7:108169937-108170152	T-47D	breast:	n/a	n/a
4	TEAD4	chr7:108169751-108170186	H1-hESC	embryonic stem cell:	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
ENSG00000135241	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000177683	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10487859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[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[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][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	0.81[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];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238841	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs13245101	0.84[EUR][1000 genomes]
rs13245242	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs13307045	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13312593	0.90[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];0.84[EUR][1000 genomes]
rs17423043	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs17423119	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs17424206	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194587	0.86[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	0.83[EUR][1000 genomes]
rs2300052	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs3202837	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33987381	0.86[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	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34887057	0.90[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[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[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40850	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40854	0.90[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];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40880	0.94[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	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]
rs40886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs40895	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40899	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[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];1.00[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];0.98[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	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40934	0.86[ASN][1000 genomes]
rs40938	0.86[ASN][1000 genomes]
rs40939	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40940	0.86[ASN][1000 genomes]
rs40941	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	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs41385644	1.00[CEU][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	0.90[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[JPT][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	0.90[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];0.81[YRI][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];0.90[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	0.82[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];0.83[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	0.85[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs40900	THAP5	cis	normal skin	skin_eQTL
rs40900	THAP5	cis	multi-tissue	Pritchard
rs40900	THAP5	cis	Muscle Skeletal	GTEx
rs40900	THAP5	cis	uninvolved skin	skin_eQTL
rs40900	THAP5	cis	Heart Left Ventricle	GTEx
rs40900	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40900	THAP5	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108167400-108173400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:108167600-108176200	Weak transcription	Primary B cells from cord blood	blood
3	chr7:108167800-108170400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:108168800-108175800	Weak transcription	K562	blood
5	chr7:108169600-108170200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:108169800-108170200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:108170000-108170200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:108170000-108170200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:108170000-108170200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr7:108170000-108170200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr7:108170000-108170200	Enhancers	HMEC	breast
12	chr7:108170000-108170600	Enhancers	Placenta	Placenta

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