Variant report

Variant	rs12643284
Chromosome Location	chr4:79971442-79971443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10518213	0.96[EUR][1000 genomes]
rs11723369	0.95[EUR][1000 genomes]
rs12499521	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1350008	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1378379	0.94[EUR][1000 genomes]
rs1455299	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1455305	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1455306	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1455307	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1480719	0.99[EUR][1000 genomes]
rs1480735	0.94[EUR][1000 genomes]
rs1480736	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1480737	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1480738	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17003589	0.97[EUR][1000 genomes]
rs17003625	0.96[EUR][1000 genomes]
rs17003626	0.96[EUR][1000 genomes]
rs188253	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs188254	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2016189	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs207020	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2127782	0.96[EUR][1000 genomes]
rs2127783	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2604827	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2604828	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2604830	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2604832	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2604833	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2604834	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2622350	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2622352	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2622353	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2622354	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2622355	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2622356	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2622357	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2622358	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs286448	0.99[EUR][1000 genomes]
rs286450	1.00[EUR][1000 genomes]
rs286452	0.99[EUR][1000 genomes]
rs286456	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs286457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs286458	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs286459	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs286460	0.97[EUR][1000 genomes]
rs286461	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs286462	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs286463	0.95[EUR][1000 genomes]
rs286464	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs286465	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs286466	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs286467	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs286468	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs286473	1.00[EUR][1000 genomes]
rs4320158	0.99[EUR][1000 genomes]
rs55672352	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56391107	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62308747	0.96[EUR][1000 genomes]
rs62308748	0.96[EUR][1000 genomes]
rs62308749	0.94[EUR][1000 genomes]
rs62310026	0.87[EUR][1000 genomes]
rs6813045	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6813727	0.96[EUR][1000 genomes]
rs6825891	0.96[EUR][1000 genomes]
rs6833006	0.96[EUR][1000 genomes]
rs6838863	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7438158	0.96[EUR][1000 genomes]
rs7685661	0.96[EUR][1000 genomes]
rs930834	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs962169	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9686053	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv879505	chr4:79887043-80293046	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3448470	chr4:79898340-80026510	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv432614	chr4:79910989-79993822	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79965600-79973200	Weak transcription	K562	blood
2	chr4:79967800-79971600	Weak transcription	Fetal Brain Female	brain
3	chr4:79967800-79979600	Weak transcription	Aorta	Aorta
4	chr4:79968000-79973800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:79969800-79973400	Enhancers	Fetal Brain Male	brain
6	chr4:79970000-79972400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr4:79970000-79975000	Weak transcription	Fetal Heart	heart
8	chr4:79970400-79971600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:79970400-79971600	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:79970400-79971800	Weak transcription	Fetal Lung	lung
11	chr4:79970400-79978200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:79970400-79978600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:79970600-79971600	Weak transcription	Brain Substantia Nigra	brain
14	chr4:79971000-79971600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:79971000-79971600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr4:79971000-79971600	Active TSS	NHDF-Ad	bronchial
17	chr4:79971000-79971800	Active TSS	Duodenum Mucosa	Duodenum
18	chr4:79971000-79972000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:79971000-79972000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:79971200-79971600	Active TSS	Colon Smooth Muscle	Colon
21	chr4:79971200-79971600	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:79971200-79972000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr4:79971200-79972000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr4:79971400-79971600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:79971400-79971800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr4:79971400-79971800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr4:79971400-79971800	Active TSS	Colonic Mucosa	Colon
28	chr4:79971400-79971800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr4:79971400-79971800	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr4:79971400-79972000	Bivalent Enhancer	Fetal Stomach	stomach
31	chr4:79971400-79972000	Enhancers	Pancreas	Pancrea
32	chr4:79971400-79972000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr4:79971400-79972200	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links