Variant report

Variant	rs12643323
Chromosome Location	chr4:2919652-2919653
allele	A/G
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:25)

rs_ID	r²[population]
rs10026792	0.81[AMR][1000 genomes]
rs1014947	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014948	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12647647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647713	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649553	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843589	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843603	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17833981	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17834203	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032470	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2096760	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3021131	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55754437	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55927173	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58115360	0.81[AMR][1000 genomes]
rs59150074	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs624833	0.83[ASN][1000 genomes]
rs6600769	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6819310	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6824567	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7436306	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655104	0.81[AMR][1000 genomes]
rs7678161	0.84[EUR][1000 genomes];0.91[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
rs12643323	GRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr4:2894000-2923000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:2894800-2919800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
5	chr4:2903000-2925400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:2907400-2935400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:2909200-2922400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:2909400-2923400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:2910600-2927800	Weak transcription	Small Intestine	intestine
10	chr4:2911200-2924000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:2911200-2935000	Weak transcription	Psoas Muscle	Psoas
12	chr4:2912600-2934800	Weak transcription	A549	lung
13	chr4:2913000-2923800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:2913000-2935000	Weak transcription	K562	blood
15	chr4:2913800-2924000	Weak transcription	Stomach Mucosa	stomach
16	chr4:2914000-2925800	Weak transcription	NHDF-Ad	bronchial
17	chr4:2914200-2925200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:2915600-2923400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:2915600-2924800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:2915600-2933000	Weak transcription	Right Atrium	heart
21	chr4:2916400-2923400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:2916400-2929800	Weak transcription	Fetal Heart	heart
23	chr4:2916600-2921800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:2916800-2920400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr4:2916800-2924200	Weak transcription	NH-A	brain
26	chr4:2916800-2924800	Weak transcription	Pancreas	Pancrea
27	chr4:2917000-2921600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:2917000-2922600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:2917000-2924000	Weak transcription	HSMM	muscle
30	chr4:2917000-2932000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:2917200-2920600	Weak transcription	GM12878-XiMat	blood
32	chr4:2917200-2924200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:2917200-2924800	Weak transcription	HepG2	liver
34	chr4:2917400-2924200	Weak transcription	HUVEC	blood vessel
35	chr4:2917400-2925000	Weak transcription	Primary B cells from cord blood	blood
36	chr4:2917400-2925000	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:2917600-2925200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:2917800-2924000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:2917800-2924200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:2917800-2924600	Weak transcription	NHEK	skin
41	chr4:2917800-2924800	Weak transcription	Colonic Mucosa	Colon
42	chr4:2917800-2924800	Weak transcription	HMEC	breast
43	chr4:2917800-2925000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:2917800-2925000	Weak transcription	Gastric	stomach
45	chr4:2917800-2925000	Weak transcription	Dnd41	blood
46	chr4:2917800-2925200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:2917800-2925400	Weak transcription	NHLF	lung
48	chr4:2917800-2926000	Weak transcription	Aorta	Aorta
49	chr4:2918000-2924200	Weak transcription	Spleen	Spleen
50	chr4:2918000-2925200	Weak transcription	HSMMtube	muscle

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