Variant report

Variant	rs249413
Chromosome Location	chr5:40721438-40721439
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	chr5:40713762..40716237-chr5:40720241..40722036,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10056345	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060234	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10064175	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1097546	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13354346	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13355305	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154268	0.85[ASN][1000 genomes]
rs154275	0.85[ASN][1000 genomes]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs171605	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs193864	0.83[ASN][1000 genomes]
rs2161521	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249414	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249416	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249420	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249422	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249423	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249425	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249428	0.85[ASN][1000 genomes]
rs249429	0.85[ASN][1000 genomes]
rs257009	0.84[ASN][1000 genomes]
rs28569300	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29743	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29744	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs369940	0.89[EUR][1000 genomes]
rs4277957	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285273	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315964	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315965	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432071	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs434778	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4383756	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447810	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453037	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4573034	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs461404	0.85[ASN][1000 genomes]
rs466108	0.85[ASN][1000 genomes]
rs466962	0.83[ASN][1000 genomes]
rs4957344	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59069340	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59920139	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451535	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451537	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871999	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896993	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708680	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726237	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7737044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs837101	0.84[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	esv3432300	chr5:40698244-40726882	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs249413	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs249413	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:40695200-40727000	Weak transcription	HSMM	muscle
6	chr5:40700800-40722200	Weak transcription	Lung	lung
7	chr5:40701000-40722200	Weak transcription	Esophagus	oesophagus
8	chr5:40705600-40727000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:40709600-40745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:40712800-40741200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:40713000-40722200	Weak transcription	Gastric	stomach
12	chr5:40713000-40722200	Weak transcription	Pancreas	Pancrea
13	chr5:40713200-40740600	Weak transcription	Right Ventricle	heart
14	chr5:40713600-40734800	Weak transcription	Hela-S3	cervix
15	chr5:40714400-40727400	Weak transcription	Brain Anterior Caudate	brain
16	chr5:40714600-40739400	Weak transcription	GM12878-XiMat	blood
17	chr5:40715400-40733600	Weak transcription	Fetal Heart	heart
18	chr5:40715400-40739400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:40715600-40734800	Weak transcription	NHEK	skin
20	chr5:40716400-40733200	Weak transcription	HUVEC	blood vessel
21	chr5:40716400-40733600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:40716400-40733800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:40716800-40724000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:40717000-40727400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:40717600-40722200	Weak transcription	Colonic Mucosa	Colon
26	chr5:40717600-40733600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:40717800-40724000	Weak transcription	A549	lung
28	chr5:40717800-40727400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:40717800-40733600	Weak transcription	Brain Substantia Nigra	brain
30	chr5:40717800-40733600	Weak transcription	NHDF-Ad	bronchial
31	chr5:40717800-40734400	Weak transcription	NH-A	brain
32	chr5:40718000-40724000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:40718000-40727000	Weak transcription	Osteobl	bone
34	chr5:40718000-40727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:40718600-40722600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:40719400-40721600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:40719400-40722800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:40719800-40722000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:40720000-40727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:40720000-40733600	Weak transcription	Fetal Kidney	kidney
41	chr5:40720400-40722400	Strong transcription	Primary T cells from cord blood	blood
42	chr5:40720400-40723600	Weak transcription	K562	blood
43	chr5:40720600-40721600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:40720600-40721600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr5:40720600-40721600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:40720600-40721600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:40720600-40721800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr5:40720600-40721800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:40720600-40721800	Strong transcription	Ovary	ovary
50	chr5:40720600-40722000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links