Variant report

Variant	rs6966107
Chromosome Location	chr7:108050767-108050768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108042175..108044661-chr7:108050644..108052443,2	K562	blood:
2	chr7:108044915..108046509-chr7:108049810..108051904,2	MCF-7	breast:
3	chr7:108044020..108046145-chr7:108049502..108052110,2	K562	blood:
4	chr7:108049821..108052079-chr7:108053231..108055054,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10245718	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs11971972	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11973105	0.84[EUR][1000 genomes]
rs11973823	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11976021	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11979596	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11983900	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12669879	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12705470	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13222628	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13227836	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13228190	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13238841	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13245101	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13245242	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17155637	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17338441	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17338462	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17421351	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17423043	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17423119	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2108252	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2108253	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2214913	0.84[EUR][1000 genomes]
rs2300036	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2300040	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300048	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300052	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2395995	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34218460	0.83[EUR][1000 genomes]
rs35429156	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35436957	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35617326	0.84[EUR][1000 genomes]
rs56145857	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59458537	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60398019	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6466224	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6466225	0.87[CEU][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6466226	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6466233	0.84[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66461825	0.84[EUR][1000 genomes]
rs67027479	0.84[EUR][1000 genomes]
rs6949637	0.84[EUR][1000 genomes]
rs6954366	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6959023	0.83[EUR][1000 genomes]
rs6959409	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960478	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6969521	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][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	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71213282	0.84[EUR][1000 genomes]
rs7784170	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7786947	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7790875	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7792321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7797885	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7806869	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7807737	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7807941	0.84[EUR][1000 genomes]
rs9649307	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6966107	THAP5	cis	normal skin	skin_eQTL
rs6966107	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108036600-108054200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:108044600-108054600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:108046800-108054200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:108047000-108054200	Weak transcription	NHLF	lung
5	chr7:108047400-108054200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:108048000-108054200	Weak transcription	HUVEC	blood vessel
7	chr7:108049200-108054200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:108049200-108054200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:108049400-108051800	Enhancers	A549	lung
10	chr7:108049400-108053600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:108049400-108053800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:108049400-108056400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:108049600-108054200	Weak transcription	Brain Angular Gyrus	brain
14	chr7:108049800-108054200	Weak transcription	Brain Anterior Caudate	brain
15	chr7:108050000-108054200	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:108050000-108054400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:108050000-108054600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:108050000-108055000	Weak transcription	Brain Germinal Matrix	brain
19	chr7:108050000-108055000	Weak transcription	Brain Substantia Nigra	brain
20	chr7:108050000-108056400	Weak transcription	Fetal Brain Female	brain
21	chr7:108050200-108054200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:108050200-108054200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:108050200-108054400	Weak transcription	Brain Hippocampus Middle	brain
24	chr7:108050200-108054400	Weak transcription	Pancreas	Pancrea
25	chr7:108050200-108055200	Weak transcription	Fetal Brain Male	brain

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