Variant report

Variant	rs13420572
Chromosome Location	chr2:179986367-179986368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10084229	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10084475	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170430	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10196577	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10205477	0.85[ASN][1000 genomes]
rs10930855	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930856	0.88[ASN][1000 genomes]
rs12693175	1.00[ASN][1000 genomes]
rs13021442	0.87[ASN][1000 genomes]
rs13022867	0.85[ASN][1000 genomes]
rs13029576	0.88[ASN][1000 genomes]
rs13396334	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403231	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13404037	0.88[ASN][1000 genomes]
rs17363260	1.00[ASN][1000 genomes]
rs17363267	1.00[ASN][1000 genomes]
rs1900338	1.00[ASN][1000 genomes]
rs2289993	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289994	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28763731	0.88[ASN][1000 genomes]
rs34728717	1.00[ASN][1000 genomes]
rs55750558	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56109193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181927	0.88[ASN][1000 genomes]
rs67028844	0.88[ASN][1000 genomes]
rs67312569	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13420572	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
4	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:179972600-180001800	Weak transcription	NHEK	skin
12	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
16	chr2:179973200-179986800	Strong transcription	Adipose Nuclei	Adipose
17	chr2:179973200-179987000	Weak transcription	Right Ventricle	heart
18	chr2:179973200-179987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:179973200-179988400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:179973200-179988800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:179973200-179989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:179973200-179989400	Weak transcription	Primary T cells from cord blood	blood
23	chr2:179973400-179990000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
25	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
26	chr2:179973400-180012600	Weak transcription	NHLF	lung
27	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:179973800-179986800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:179974400-179994200	Strong transcription	HepG2	liver
30	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
32	chr2:179976600-179989800	Weak transcription	Gastric	stomach
33	chr2:179977200-179988000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:179977400-179987400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:179977400-179987800	Weak transcription	Brain Angular Gyrus	brain
36	chr2:179977400-179988400	Weak transcription	Brain Substantia Nigra	brain
37	chr2:179977400-180004400	Weak transcription	Lung	lung
38	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
39	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
40	chr2:179977600-179988600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:179977800-179988600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
45	chr2:179979400-179988600	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:179980000-180038800	Weak transcription	HMEC	breast
47	chr2:179980000-180056800	Weak transcription	HSMM	muscle
48	chr2:179980400-179989400	Weak transcription	Thymus	Thymus
49	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood

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