Variant report

Variant	rs1580297
Chromosome Location	chr4:76403786-76403787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029348	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10031553	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1046662	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728327	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11729929	0.82[AMR][1000 genomes]
rs11730978	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11735018	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11935932	0.90[EUR][1000 genomes]
rs13112378	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13145288	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1351092	0.94[EUR][1000 genomes]
rs1389443	0.94[EUR][1000 genomes]
rs1395359	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1395360	0.81[EUR][1000 genomes]
rs1478174	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564174	0.93[EUR][1000 genomes]
rs1600100	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1676917	0.94[EUR][1000 genomes]
rs1817387	0.96[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1841932	0.95[CEU][hapmap];0.88[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]
rs1841934	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2045863	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2126855	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28507535	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867921	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4593160	0.84[EUR][1000 genomes]
rs4859963	0.85[EUR][1000 genomes]
rs59581284	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6535523	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6815241	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816603	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6823674	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829753	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6833496	0.91[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6835579	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841171	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs6841882	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7661659	0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7664140	0.95[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7698352	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786682	0.94[EUR][1000 genomes]
rs786684	0.94[EUR][1000 genomes]
rs786688	0.91[CEU][hapmap]
rs9041	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs949611	0.84[EUR][1000 genomes]
rs955545	0.85[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1580297	THAP6	cis	Lymphoblastoid	GTEx
rs1580297	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76394000-76406200	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:76394000-76406600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
5	chr4:76395400-76405200	Weak transcription	Fetal Heart	heart
6	chr4:76395600-76405800	Weak transcription	Brain Germinal Matrix	brain
7	chr4:76395800-76406600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
9	chr4:76395800-76437000	Weak transcription	Lung	lung
10	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
11	chr4:76396200-76424400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
13	chr4:76397000-76405200	Weak transcription	NHEK	skin
14	chr4:76397200-76403800	Weak transcription	HUVEC	blood vessel
15	chr4:76397200-76405200	Weak transcription	Left Ventricle	heart
16	chr4:76397200-76414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:76397400-76403800	Weak transcription	GM12878-XiMat	blood
18	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:76398200-76405600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:76398200-76415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:76398400-76407400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:76398600-76405600	Weak transcription	NHLF	lung
24	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr4:76400600-76403800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
28	chr4:76400800-76404800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:76400800-76405200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:76400800-76405200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:76400800-76405600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:76400800-76406600	Weak transcription	HMEC	breast
33	chr4:76400800-76409200	Weak transcription	Thymus	Thymus
34	chr4:76401000-76405400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:76401000-76405400	Weak transcription	Colonic Mucosa	Colon
36	chr4:76401000-76406600	Weak transcription	Hela-S3	cervix
37	chr4:76401000-76410800	Weak transcription	HSMMtube	muscle
38	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
39	chr4:76401200-76403800	Weak transcription	Fetal Intestine Large	intestine
40	chr4:76401200-76405200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:76401200-76405200	Weak transcription	Brain Substantia Nigra	brain
42	chr4:76401200-76406000	Weak transcription	Fetal Brain Male	brain
43	chr4:76401200-76406400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr4:76401200-76409200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:76401200-76410800	Weak transcription	Stomach Mucosa	stomach
46	chr4:76401200-76411400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:76401800-76404200	Strong transcription	Fetal Lung	lung
48	chr4:76401800-76412400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:76402000-76403800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:76402000-76411600	Strong transcription	HSMM	muscle

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