Variant report

Variant	rs13145288
Chromosome Location	chr4:76425189-76425190
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76420847..76422620-chr4:76423931..76425641,2	K562	blood:
2	chr4:76422807..76425261-chr4:76435739..76438350,2	MCF-7	breast:
3	chr4:76423980..76426785-chr4:76427353..76430216,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10029348	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046662	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728327	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729929	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730978	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735018	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112378	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351092	0.80[EUR][1000 genomes]
rs1389443	0.80[EUR][1000 genomes]
rs1478174	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1580297	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1600100	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1676917	0.80[EUR][1000 genomes]
rs1817387	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841932	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841934	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045863	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126855	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28507535	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867920	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867921	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59581284	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535523	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815241	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816603	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823674	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6829753	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835579	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841882	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661659	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664140	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698352	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs786682	0.80[EUR][1000 genomes]
rs786684	0.80[EUR][1000 genomes]
rs9041	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13145288	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
3	chr4:76395800-76437000	Weak transcription	Lung	lung
4	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
5	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
6	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
11	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
12	chr4:76402200-76425800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr4:76402400-76425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:76403800-76433600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:76405600-76434400	Weak transcription	Fetal Heart	heart
16	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
19	chr4:76409400-76425800	Strong transcription	Fetal Thymus	thymus
20	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:76410400-76425600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr4:76411400-76435400	Weak transcription	Small Intestine	intestine
23	chr4:76414600-76427000	Weak transcription	Fetal Stomach	stomach
24	chr4:76414600-76429400	Weak transcription	HSMMtube	muscle
25	chr4:76415200-76428200	Weak transcription	A549	lung
26	chr4:76415400-76430200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:76415400-76435600	Weak transcription	Brain Substantia Nigra	brain
28	chr4:76415400-76436400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:76415800-76430200	Weak transcription	Colonic Mucosa	Colon
30	chr4:76416000-76429400	Weak transcription	Left Ventricle	heart
31	chr4:76416600-76426600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:76416600-76436200	Weak transcription	Brain Anterior Caudate	brain
33	chr4:76416600-76437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:76417600-76436800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr4:76418000-76428400	Weak transcription	NH-A	brain
36	chr4:76418400-76427800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:76419000-76426000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr4:76419600-76429400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:76421200-76433600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:76421400-76437000	Weak transcription	Stomach Mucosa	stomach
41	chr4:76421800-76427800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:76422000-76426400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:76422000-76428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:76422400-76433800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr4:76422400-76434800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr4:76422600-76432600	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:76422800-76425200	Weak transcription	NHEK	skin
48	chr4:76422800-76426800	Weak transcription	HUVEC	blood vessel
49	chr4:76423000-76429000	Weak transcription	K562	blood
50	chr4:76423000-76431400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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