Variant report

Variant	rs820826
Chromosome Location	chr5:74002331-74002332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:73981038..73983852-chr5:73999852..74002635,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1043968	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10515191	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1104272	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11742460	0.81[EUR][1000 genomes]
rs11742621	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11743655	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11746757	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11948188	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs15694	0.83[EUR][1000 genomes]
rs2084115	0.81[EUR][1000 genomes]
rs2314936	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2314937	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5020673	0.83[EUR][1000 genomes]
rs55870102	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56365996	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59110717	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62366408	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62366417	0.81[EUR][1000 genomes]
rs6453075	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6453077	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6453084	0.83[EUR][1000 genomes]
rs6861730	0.81[EUR][1000 genomes]
rs6874609	0.83[EUR][1000 genomes]
rs6879781	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs820826	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs820826	NSA2	cis	Artery Aorta	GTEx
rs820826	NSA2	cis	Nerve Tibial	GTEx
rs820826	NSA2	cis	Adipose Subcutaneous	GTEx
rs820826	NSA2	cis	Muscle Skeletal	GTEx
rs820826	NSA2	cis	Esophagus Muscularis	GTEx
rs820826	NSA2	cis	lung	GTEx
rs820826	NSA2	cis	Heart Left Ventricle	GTEx
rs820826	NSA2	cis	Thyroid	GTEx
rs820826	NSA2	cis	Esophagus Mucosa	GTEx
rs820826	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs820826	NSA2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74017400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
4	chr5:73983000-74017400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:73983000-74027000	Weak transcription	Fetal Heart	heart
6	chr5:73983200-74030200	Weak transcription	Small Intestine	intestine
7	chr5:73983400-74016000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:73984600-74002600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:73985000-74002600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr5:73985200-74002600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:73987200-74017400	Weak transcription	Fetal Kidney	kidney
12	chr5:73987600-74014800	Weak transcription	Fetal Lung	lung
13	chr5:73988400-74021000	Weak transcription	Right Ventricle	heart
14	chr5:73989800-74002600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:73990000-74016200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:73990400-74013600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:73991800-74002400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:73993400-74014400	Weak transcription	Stomach Mucosa	stomach
19	chr5:73993400-74017400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:73993800-74014600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:73993800-74014600	Weak transcription	HSMMtube	muscle
22	chr5:73993800-74019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:73995000-74009800	Weak transcription	HMEC	breast
24	chr5:73996800-74002600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:73997600-74002600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:73997600-74002600	Strong transcription	Adipose Nuclei	Adipose
27	chr5:73998200-74002400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:73998200-74002600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:73998200-74002600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:73998200-74002600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:73998200-74002600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:73998200-74002600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:73998200-74002600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr5:73998400-74002600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:73998400-74002600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:73998400-74002600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:73998400-74002600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:73998800-74013800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:73999000-74002600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
40	chr5:73999000-74002600	Strong transcription	Colonic Mucosa	Colon
41	chr5:73999000-74002600	Strong transcription	Left Ventricle	heart
42	chr5:73999400-74002600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:73999600-74014600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr5:73999600-74015000	Weak transcription	HepG2	liver
45	chr5:73999600-74016000	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:73999800-74002400	Weak transcription	Fetal Stomach	stomach
47	chr5:73999800-74010200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:73999800-74014200	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:73999800-74014200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr5:73999800-74014800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links