Variant report

Variant	rs8029562
Chromosome Location	chr15:78343620-78343621
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78333663..78335514-chr15:78341566..78343908,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78342467-78345090	ucscGeneNc_uc002bfo_2

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004855	0.82[EUR][1000 genomes]
rs11631578	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634607	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11852768	0.93[ASN][1000 genomes]
rs12148365	0.92[ASN][1000 genomes]
rs12591418	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594823	0.86[AFR][1000 genomes]
rs12899061	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901812	0.92[ASN][1000 genomes]
rs12907701	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12907814	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911332	0.80[EUR][1000 genomes]
rs12916362	0.93[ASN][1000 genomes]
rs1348257	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1442293	0.91[ASN][1000 genomes]
rs1837913	0.91[ASN][1000 genomes]
rs2867985	0.90[ASN][1000 genomes]
rs2903702	0.93[ASN][1000 genomes]
rs3803380	0.88[ASN][1000 genomes]
rs4886553	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886554	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886555	0.90[ASN][1000 genomes]
rs4886994	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886996	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886999	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887000	0.93[ASN][1000 genomes]
rs56317829	0.88[ASN][1000 genomes]
rs57220134	0.91[ASN][1000 genomes]
rs58578288	0.92[ASN][1000 genomes]
rs62011511	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166819	0.93[ASN][1000 genomes]
rs7170746	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173128	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181594	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9047	0.90[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:78321200-78343800	Weak transcription	NHEK	skin
7	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:78331200-78344400	Weak transcription	Psoas Muscle	Psoas
9	chr15:78331400-78348600	Weak transcription	A549	lung
10	chr15:78331600-78348600	Weak transcription	K562	blood
11	chr15:78336600-78344400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:78337000-78347800	Weak transcription	Ovary	ovary
13	chr15:78337200-78344400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:78337800-78344600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:78338200-78344400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr15:78338600-78345400	Enhancers	Duodenum Mucosa	Duodenum
17	chr15:78338800-78344600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:78338800-78344800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:78338800-78347000	Genic enhancers	Fetal Thymus	thymus
20	chr15:78339000-78344800	Enhancers	Colon Smooth Muscle	Colon
21	chr15:78339000-78345000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:78339000-78345000	Enhancers	Small Intestine	intestine
23	chr15:78339000-78345200	Genic enhancers	Fetal Stomach	stomach
24	chr15:78339000-78345400	Enhancers	Primary B cells from cord blood	blood
25	chr15:78339000-78346400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr15:78339200-78344800	Enhancers	Brain Angular Gyrus	brain
27	chr15:78339200-78344800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr15:78339400-78344600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:78339800-78343800	Enhancers	HUVEC	blood vessel
30	chr15:78340000-78343800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr15:78340000-78345200	Enhancers	Right Atrium	heart
32	chr15:78340000-78345200	Enhancers	NH-A	brain
33	chr15:78340200-78344800	Enhancers	Brain Hippocampus Middle	brain
34	chr15:78340400-78344000	Weak transcription	HepG2	liver
35	chr15:78340600-78343800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:78340600-78344400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:78340800-78344400	Weak transcription	Gastric	stomach
38	chr15:78340800-78346200	Genic enhancers	Liver	Liver
39	chr15:78341200-78345200	Genic enhancers	Fetal Lung	lung
40	chr15:78341400-78343800	Enhancers	Right Ventricle	heart
41	chr15:78341400-78344400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr15:78341400-78344800	Weak transcription	Esophagus	oesophagus
43	chr15:78341400-78344800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr15:78341400-78345600	Enhancers	Brain Cingulate Gyrus	brain
45	chr15:78341800-78343800	Enhancers	Fetal Brain Male	brain
46	chr15:78341800-78344000	Enhancers	Placenta	Placenta
47	chr15:78341800-78344800	Enhancers	Fetal Brain Female	brain
48	chr15:78341800-78345600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:78342000-78343800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:78342000-78344400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links