Variant report

Variant	rs10029348
Chromosome Location	chr4:76395852-76395853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10031553	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1046662	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11728327	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730978	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11735018	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11935932	0.91[EUR][1000 genomes]
rs13112378	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13145288	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1351092	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1389443	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1395359	0.82[EUR][1000 genomes]
rs1395360	0.82[EUR][1000 genomes]
rs1478174	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564174	0.93[EUR][1000 genomes]
rs1580297	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1600100	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676917	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1817387	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841932	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841934	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045863	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2126855	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28507535	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867920	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867921	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4593160	0.85[EUR][1000 genomes]
rs4859963	0.86[EUR][1000 genomes]
rs59581284	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535523	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6815241	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6816603	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6823674	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829753	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6833496	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6835579	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841171	0.82[EUR][1000 genomes]
rs6841882	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7661659	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664140	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7698352	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs786682	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs786684	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9041	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs949611	0.85[EUR][1000 genomes]
rs955545	0.85[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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998511	chr4:76184807-76398377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10029348	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76391800-76396800	Weak transcription	HSMM	muscle
2	chr4:76392000-76396200	Weak transcription	Primary B cells from cord blood	blood
3	chr4:76392000-76402400	Weak transcription	Liver	Liver
4	chr4:76392600-76434800	Weak transcription	Gastric	stomach
5	chr4:76392800-76403000	Weak transcription	Fetal Brain Female	brain
6	chr4:76394000-76406200	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:76394000-76406600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
9	chr4:76395000-76401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:76395200-76397200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr4:76395400-76397000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:76395400-76402200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:76395400-76405200	Weak transcription	Fetal Heart	heart
14	chr4:76395600-76405800	Weak transcription	Brain Germinal Matrix	brain
15	chr4:76395800-76396800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:76395800-76397000	Weak transcription	Psoas Muscle	Psoas
17	chr4:76395800-76399200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:76395800-76402200	Weak transcription	Primary T cells from cord blood	blood
19	chr4:76395800-76402400	Weak transcription	Ovary	ovary
20	chr4:76395800-76406600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
22	chr4:76395800-76437000	Weak transcription	Lung	lung
23	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea

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