Variant report

Variant	rs2300052
Chromosome Location	chr7:108088494-108088495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108087694..108090999-chr7:108091222..108094694,3	K562	blood:
2	chr7:108084971..108087877-chr7:108088105..108090258,2	K562	blood:
3	chr7:108087694..108090660-chr7:108091222..108093377,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10245718	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs10487859	0.89[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs11971972	0.84[EUR][1000 genomes]
rs11973105	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973823	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11974559	0.89[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs11976021	0.89[GIH][hapmap];0.84[EUR][1000 genomes]
rs11979596	0.84[EUR][1000 genomes]
rs11981670	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs11983900	0.81[EUR][1000 genomes]
rs12669879	0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs12705470	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227836	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13228190	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13229488	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs13238841	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13245101	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245242	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]
rs13307045	0.86[EUR][1000 genomes]
rs13312593	0.86[EUR][1000 genomes]
rs17155637	0.88[GIH][hapmap];0.88[MEX][hapmap];0.83[YRI][hapmap]
rs17155828	0.87[EUR][1000 genomes]
rs17338441	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17338462	1.00[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17421351	0.89[GIH][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17423043	1.00[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17423119	1.00[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17424206	0.88[EUR][1000 genomes]
rs194587	0.88[EUR][1000 genomes]
rs2108252	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2108253	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2214913	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214914	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214915	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300040	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2300048	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2395995	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3202837	0.87[EUR][1000 genomes]
rs33987381	0.91[EUR][1000 genomes]
rs34218460	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34333829	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34583262	0.91[EUR][1000 genomes]
rs34814097	0.87[EUR][1000 genomes]
rs34887057	0.87[EUR][1000 genomes]
rs35429156	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35436957	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35617326	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880371	0.83[EUR][1000 genomes]
rs40843	0.89[JPT][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs40845	0.89[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs40850	0.88[EUR][1000 genomes]
rs40854	0.85[EUR][1000 genomes]
rs40872	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs40875	0.86[EUR][1000 genomes]
rs40878	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs40880	0.83[EUR][1000 genomes]
rs40885	0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs40886	0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs40895	0.84[EUR][1000 genomes]
rs40899	0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs40900	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs40901	0.84[EUR][1000 genomes]
rs40902	0.89[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs40908	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs40910	0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs41385644	0.85[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs4992578	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56145857	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59458537	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60398019	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60426977	0.86[EUR][1000 genomes]
rs6466224	0.82[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6466225	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6466226	0.89[GIH][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6466233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6466238	0.89[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs66461825	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67027479	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67694466	0.86[EUR][1000 genomes]
rs6947492	0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs6949637	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954366	0.84[EUR][1000 genomes]
rs6955152	0.88[EUR][1000 genomes]
rs6959023	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959409	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6960478	0.83[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs6966107	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6967368	0.83[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6969521	0.84[EUR][1000 genomes]
rs6976309	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976649	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976659	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976752	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976776	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976804	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978552	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71213282	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7786947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7792321	0.84[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap]
rs7797885	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7806869	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7807737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807941	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811808	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9649307	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649308	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9785056	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2300052	THAP5	cis	multi-tissue	Pritchard
rs2300052	CDHR3	cis	cerebellum	SCAN
rs2300052	THAP5	cis	normal skin	skin_eQTL
rs2300052	THAP5	cis	Esophagus Muscularis	GTEx
rs2300052	THAP5	cis	lymphoblastoid	seeQTL
rs2300052	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108067800-108089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:108068000-108089400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:108075800-108089400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:108076200-108094800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:108081600-108089800	Weak transcription	Brain Anterior Caudate	brain
6	chr7:108082800-108089400	Weak transcription	Brain Angular Gyrus	brain
7	chr7:108083400-108089400	Weak transcription	HUVEC	blood vessel
8	chr7:108084000-108089400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:108087000-108089200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:108087000-108089200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:108087800-108088800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:108087800-108090000	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:108088000-108089000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:108088000-108089000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr7:108088000-108089000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr7:108088200-108088600	Enhancers	Fetal Brain Female	brain
17	chr7:108088200-108089400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:108088200-108091800	Enhancers	A549	lung
19	chr7:108088400-108088600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:108088400-108089000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:108088400-108090200	Enhancers	Fetal Lung	lung
22	chr7:108088400-108090400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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