Variant report

Variant	rs1263343
Chromosome Location	chr4:2923816-2923817
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1012365	0.85[ASN][1000 genomes]
rs1242228	0.82[EUR][1000 genomes]
rs1263338	0.82[ASN][1000 genomes]
rs1263339	0.83[ASN][1000 genomes]
rs1263341	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1263342	0.85[ASN][1000 genomes]
rs1263344	0.85[ASN][1000 genomes]
rs1263348	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1263359	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1263360	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13140733	0.93[ASN][1000 genomes]
rs2004973	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2798287	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775067	0.85[AFR][1000 genomes]
rs3775068	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4690004	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4690005	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4963	0.84[ASN][1000 genomes]
rs762847	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1263343	GRK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
2	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
3	chr4:2903000-2925400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:2910600-2927800	Weak transcription	Small Intestine	intestine
6	chr4:2911200-2924000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
8	chr4:2912600-2934800	Weak transcription	A549	lung
9	chr4:2913000-2935000	Weak transcription	K562	blood
10	chr4:2913800-2924000	Weak transcription	Stomach Mucosa	stomach
11	chr4:2914000-2925800	Weak transcription	NHDF-Ad	bronchial
12	chr4:2914200-2925200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:2915600-2924800	Weak transcription	Brain Substantia Nigra	brain
14	chr4:2915600-2933000	Weak transcription	Right Atrium	heart
15	chr4:2916400-2929800	Weak transcription	Fetal Heart	heart
16	chr4:2916800-2924200	Weak transcription	NH-A	brain
17	chr4:2916800-2924800	Weak transcription	Pancreas	Pancrea
18	chr4:2917000-2924000	Weak transcription	HSMM	muscle
19	chr4:2917000-2932000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:2917200-2924200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:2917200-2924800	Weak transcription	HepG2	liver
22	chr4:2917400-2924200	Weak transcription	HUVEC	blood vessel
23	chr4:2917400-2925000	Weak transcription	Primary B cells from cord blood	blood
24	chr4:2917400-2925000	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:2917600-2925200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:2917800-2924000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:2917800-2924200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:2917800-2924600	Weak transcription	NHEK	skin
29	chr4:2917800-2924800	Weak transcription	Colonic Mucosa	Colon
30	chr4:2917800-2924800	Weak transcription	HMEC	breast
31	chr4:2917800-2925000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:2917800-2925000	Weak transcription	Gastric	stomach
33	chr4:2917800-2925000	Weak transcription	Dnd41	blood
34	chr4:2917800-2925200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:2917800-2925400	Weak transcription	NHLF	lung
36	chr4:2917800-2926000	Weak transcription	Aorta	Aorta
37	chr4:2918000-2924200	Weak transcription	Spleen	Spleen
38	chr4:2918000-2925200	Weak transcription	HSMMtube	muscle
39	chr4:2918400-2925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:2918600-2924000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:2918600-2924000	Weak transcription	Esophagus	oesophagus
42	chr4:2918600-2924000	Weak transcription	Lung	lung
43	chr4:2918600-2924200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:2918600-2924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr4:2918600-2924200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:2918600-2924200	Weak transcription	Fetal Stomach	stomach
47	chr4:2918600-2924200	Weak transcription	Ovary	ovary
48	chr4:2918600-2924600	Weak transcription	Left Ventricle	heart
49	chr4:2918800-2924000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr4:2918800-2924000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links