Variant report

Variant	rs6841882
Chromosome Location	chr4:76413745-76413746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10029348	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031553	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.97[MKK][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728327	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729290	0.82[GIH][hapmap]
rs11729929	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735018	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112378	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145288	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351092	0.81[EUR][1000 genomes]
rs1389443	0.81[EUR][1000 genomes]
rs1395359	0.96[CEU][hapmap]
rs1478174	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1580297	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1600100	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1676917	0.81[EUR][1000 genomes]
rs1817387	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841932	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045863	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126855	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28507535	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867920	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59581284	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535523	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815241	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816603	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823674	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6829753	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833496	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841171	0.96[CEU][hapmap]
rs7661659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664140	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698352	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs786682	0.81[EUR][1000 genomes]
rs786684	0.81[EUR][1000 genomes]
rs786688	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs9041	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9998529	0.80[GIH][hapmap]

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	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
3	esv3378956	chr4:76411853-76414301	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6841882	THAP6	cis	Lymphoblastoid	GTEx
rs6841882	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
3	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
4	chr4:76395800-76437000	Weak transcription	Lung	lung
5	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
6	chr4:76396200-76424400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
8	chr4:76397200-76414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:76398200-76415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
15	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
16	chr4:76402000-76418600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:76402200-76422000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:76402200-76423000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:76402200-76425800	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr4:76402400-76418400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:76402400-76418800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:76402400-76419200	Strong transcription	Liver	Liver
23	chr4:76402400-76425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:76402600-76423200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:76402800-76417600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:76403000-76423800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:76403600-76418800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:76403800-76433600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:76404200-76419400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:76404400-76419600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:76404400-76422800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:76404800-76418400	Strong transcription	Placenta	Placenta
33	chr4:76404800-76422800	Strong transcription	Dnd41	blood
34	chr4:76405400-76422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:76405600-76434400	Weak transcription	Fetal Heart	heart
36	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:76406400-76413800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:76407600-76415000	Weak transcription	Brain Germinal Matrix	brain
40	chr4:76407800-76414000	Weak transcription	NHEK	skin
41	chr4:76407800-76414400	Weak transcription	Brain Substantia Nigra	brain
42	chr4:76407800-76414400	Weak transcription	Colonic Mucosa	Colon
43	chr4:76407800-76414400	Weak transcription	NHLF	lung
44	chr4:76407800-76424600	Weak transcription	Fetal Brain Male	brain
45	chr4:76408000-76416600	Weak transcription	HepG2	liver
46	chr4:76408000-76424600	Weak transcription	Ovary	ovary
47	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
48	chr4:76409000-76415400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:76409400-76414800	Weak transcription	K562	blood
50	chr4:76409400-76425800	Strong transcription	Fetal Thymus	thymus

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