Variant report

Variant	rs6425600
Chromosome Location	chr1:172024033-172024034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10489730	0.94[ASN][1000 genomes]
rs10797716	0.93[ASN][1000 genomes]
rs10797719	0.94[ASN][1000 genomes]
rs10797720	0.94[ASN][1000 genomes]
rs10797725	0.94[ASN][1000 genomes]
rs10797735	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10797736	0.95[EUR][1000 genomes]
rs10910938	0.92[EUR][1000 genomes]
rs10910945	0.92[EUR][1000 genomes]
rs12037820	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12038713	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12117623	0.82[EUR][1000 genomes]
rs12119190	0.80[EUR][1000 genomes]
rs12128720	0.96[ASN][1000 genomes]
rs1555382	0.94[ASN][1000 genomes]
rs1555383	0.94[ASN][1000 genomes]
rs2038481	0.93[ASN][1000 genomes]
rs2057302	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057303	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2208367	0.94[ASN][1000 genomes]
rs2295610	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2295611	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36178280	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36180993	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4076678	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4333881	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4489594	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4916241	0.94[ASN][1000 genomes]
rs4916413	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425599	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669406	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683503	0.93[ASN][1000 genomes]
rs6700538	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7518865	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519236	0.94[ASN][1000 genomes]
rs7530970	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533694	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172006400-172025600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:172010600-172051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:172010800-172037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:172011400-172037800	Weak transcription	Ovary	ovary
5	chr1:172014200-172024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:172014600-172024400	Weak transcription	Brain Germinal Matrix	brain
7	chr1:172015000-172024200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:172015000-172033200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:172015000-172042600	Weak transcription	Fetal Brain Female	brain
10	chr1:172015200-172026000	Weak transcription	Aorta	Aorta
11	chr1:172015200-172032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:172016600-172037800	Weak transcription	Brain Substantia Nigra	brain
13	chr1:172019000-172024200	Weak transcription	Brain Anterior Caudate	brain
14	chr1:172020200-172024400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:172020200-172038800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:172020200-172040600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:172021400-172024200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:172021400-172026600	Weak transcription	Left Ventricle	heart
19	chr1:172023400-172024600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:172023600-172024200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links