Variant report

Variant	rs28670000
Chromosome Location	chr7:128188991-128188992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10230632	0.82[ASN][1000 genomes]
rs10230965	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10232401	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10243297	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10245559	0.82[ASN][1000 genomes]
rs10246093	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246261	0.83[EUR][1000 genomes]
rs10251475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10251597	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10271590	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12381410	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12386692	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28479078	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28525628	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28526579	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28788212	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs339075	0.82[ASN][1000 genomes]
rs3958071	0.82[ASN][1000 genomes]
rs4642561	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5009156	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs58979384	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467190	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6943009	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73463166	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73465114	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7797240	0.86[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	esv1848097	chr7:128179503-128248497	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28670000	RP11-274B21.4	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172600-128189800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:128172600-128191000	Weak transcription	Ovary	ovary
3	chr7:128172600-128191200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:128172600-128193400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:128172600-128210800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:128172600-128214800	Weak transcription	Gastric	stomach
7	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
8	chr7:128173000-128190400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:128173000-128190800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:128173000-128231800	Weak transcription	Colonic Mucosa	Colon
11	chr7:128173000-128231800	Weak transcription	Fetal Kidney	kidney
12	chr7:128173600-128201000	Weak transcription	Psoas Muscle	Psoas
13	chr7:128173600-128214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:128173800-128190800	Weak transcription	Brain Substantia Nigra	brain
15	chr7:128173800-128191000	Weak transcription	Brain Angular Gyrus	brain
16	chr7:128173800-128197800	Weak transcription	Right Atrium	heart
17	chr7:128173800-128199800	Weak transcription	Right Ventricle	heart
18	chr7:128173800-128201000	Weak transcription	Brain Germinal Matrix	brain
19	chr7:128173800-128214800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr7:128174000-128210600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:128174000-128220600	Weak transcription	NHLF	lung
23	chr7:128174000-128231800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:128174000-128232600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:128174200-128190200	Weak transcription	HepG2	liver
26	chr7:128174200-128191600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:128174600-128193600	Strong transcription	Fetal Stomach	stomach
28	chr7:128175400-128231800	Weak transcription	Left Ventricle	heart
29	chr7:128175800-128193600	Strong transcription	Fetal Intestine Small	intestine
30	chr7:128176000-128214800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:128176200-128190000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:128177600-128231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:128177800-128191400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:128179000-128189200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:128179200-128231800	Weak transcription	Esophagus	oesophagus
36	chr7:128180400-128189200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:128181800-128231800	Weak transcription	Aorta	Aorta
38	chr7:128182800-128190000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:128183000-128201000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:128183000-128214200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:128183200-128191800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:128183400-128214800	Weak transcription	HUVEC	blood vessel
43	chr7:128183600-128190600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:128183600-128196200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:128183600-128214800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:128183800-128189000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:128183800-128189000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:128184200-128189200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:128184800-128189200	Strong transcription	Fetal Intestine Large	intestine
50	chr7:128184800-128192000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links