Variant report

Variant	rs2078020
Chromosome Location	chr3:67619472-67619473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1028950	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11711916	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12485966	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12488912	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1576398	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1590875	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17808406	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974109	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2634725	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2634729	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2634735	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4856878	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56033013	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56157830	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56193099	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57578558	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59116776	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59816011	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60923125	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62256409	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6797488	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7618449	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2078020	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
2	chr3:67578200-67634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:67579200-67620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:67579400-67623000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:67579400-67633800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:67579400-67657600	Weak transcription	Pancreas	Pancrea
7	chr3:67580800-67620200	Weak transcription	GM12878-XiMat	blood
8	chr3:67582200-67637000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:67582400-67620400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:67587000-67620200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:67587400-67628000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:67591400-67620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:67594000-67620600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:67594000-67631000	Weak transcription	K562	blood
15	chr3:67595000-67639400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:67596400-67629000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:67598000-67644200	Weak transcription	NHLF	lung
18	chr3:67599600-67620800	Weak transcription	Dnd41	blood
19	chr3:67599600-67621000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:67599600-67629000	Weak transcription	Right Ventricle	heart
21	chr3:67600200-67628800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:67600400-67620600	Weak transcription	HMEC	breast
23	chr3:67600400-67624400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:67600800-67621000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:67601800-67673000	Weak transcription	Fetal Heart	heart
26	chr3:67602200-67619800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:67602200-67620800	Weak transcription	Fetal Stomach	stomach
28	chr3:67602200-67644200	Weak transcription	Gastric	stomach
29	chr3:67602200-67654800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:67602200-67655400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:67602200-67656000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:67602400-67624000	Weak transcription	Psoas Muscle	Psoas
33	chr3:67602400-67646200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:67602600-67635600	Weak transcription	Aorta	Aorta
35	chr3:67607000-67626200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:67609200-67620200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:67609200-67620600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:67609200-67621200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:67609200-67624400	Weak transcription	Left Ventricle	heart
40	chr3:67609200-67637000	Weak transcription	Ovary	ovary
41	chr3:67609400-67620600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:67609400-67644000	Weak transcription	NHDF-Ad	bronchial
43	chr3:67609800-67620800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:67609800-67620800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:67609800-67621000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:67610000-67628200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:67610200-67620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:67610400-67620600	Weak transcription	Fetal Intestine Large	intestine
49	chr3:67611000-67620200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr3:67612200-67621000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links