Variant report

Variant	rs40910
Chromosome Location	chr7:108177242-108177243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:108164488..108174629-chr7:108175608..108181939,14	K562	blood:
2	chr7:108174829..108177783-chr7:108186368..108189092,2	K562	blood:
3	chr7:108172423..108174629-chr7:108175217..108177443,4	K562	blood:
4	chr7:108175375..108182018-chr7:108207477..108213332,11	K562	blood:
5	chr7:108174082..108182018-chr7:108207303..108212626,11	K562	blood:
6	chr7:108165819..108168153-chr7:108175715..108177570,2	MCF-7	breast:
7	chr7:108175296..108178679-chr7:108201125..108203447,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177683	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000128590	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10487859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973105	0.83[EUR][1000 genomes]
rs11974559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12666562	0.86[ASN][1000 genomes]
rs12705470	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs13228190	0.81[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];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238841	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs13245101	0.83[EUR][1000 genomes]
rs13245242	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs13307045	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13312593	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17155828	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17338441	0.83[EUR][1000 genomes]
rs17338462	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs17423043	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs17423119	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs17424206	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194587	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214913	0.83[EUR][1000 genomes]
rs2214914	0.87[EUR][1000 genomes]
rs2214915	0.88[EUR][1000 genomes]
rs2300048	0.81[EUR][1000 genomes]
rs2300052	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs3202837	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33987381	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34218460	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.90[EUR][1000 genomes]
rs34814097	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34887057	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35372181	0.88[ASN][1000 genomes]
rs35436957	0.81[EUR][1000 genomes]
rs35617326	0.83[EUR][1000 genomes]
rs35880371	0.95[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];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40850	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40854	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40875	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40880	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40882	0.86[AMR][1000 genomes];0.90[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40895	0.88[AMR][1000 genomes];0.98[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];0.96[AFR][1000 genomes];0.98[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40901	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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];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];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4992578	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.80[EUR][1000 genomes]
rs59458537	0.81[EUR][1000 genomes]
rs60426977	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466233	0.81[EUR][1000 genomes]
rs6466238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461825	0.83[EUR][1000 genomes]
rs67027479	0.83[EUR][1000 genomes]
rs67694466	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6947492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949637	0.83[EUR][1000 genomes]
rs6955152	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959023	0.82[EUR][1000 genomes]
rs6967368	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs6976309	0.83[EUR][1000 genomes]
rs6976649	0.82[EUR][1000 genomes]
rs6976659	0.83[EUR][1000 genomes]
rs6976752	0.83[EUR][1000 genomes]
rs6976776	0.83[EUR][1000 genomes]
rs6976804	0.83[EUR][1000 genomes]
rs6978552	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs71213282	0.83[EUR][1000 genomes]
rs71568528	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs7786947	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs7790875	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs7806869	0.81[EUR][1000 genomes]
rs7807737	0.83[EUR][1000 genomes]
rs7807941	0.83[EUR][1000 genomes]
rs7811808	0.84[EUR][1000 genomes]
rs9649307	0.83[EUR][1000 genomes]
rs9649308	0.83[EUR][1000 genomes]
rs9785056	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv275106	chr7:108173123-108179506	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs40910	THAP5	cis	Esophagus Muscularis	GTEx
rs40910	THAP5	cis	uninvolved skin	skin_eQTL
rs40910	THAP5	cis	multi-tissue	Pritchard
rs40910	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40910	THAP5	cis	Muscle Skeletal	GTEx
rs40910	THAP5	cis	Heart Left Ventricle	GTEx
rs40910	THAP5	cis	normal skin	skin_eQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108176200-108178800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr7:108176400-108178200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:108176600-108178600	Weak transcription	Primary B cells from cord blood	blood
4	chr7:108176800-108178000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:108177000-108177600	Enhancers	K562	blood
6	chr7:108177200-108177600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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