Variant report

Variant	rs6421497
Chromosome Location	chr1:56923735-56923736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10888971	0.83[ASN][1000 genomes]
rs10888972	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11206815	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1261410	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1261412	1.00[CHB][hapmap]
rs1271160	0.86[AMR][1000 genomes]
rs1319274	1.00[CHB][hapmap]
rs1361823	1.00[CHB][hapmap]
rs17407790	1.00[CHB][hapmap]
rs1777276	1.00[CHB][hapmap]
rs1815487	0.87[ASN][1000 genomes]
rs1889145	0.91[EUR][1000 genomes]
rs1964940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184104	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2780292	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2780857	0.91[ASN][1000 genomes]
rs4912286	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6588633	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588634	0.87[ASN][1000 genomes]
rs6588635	0.87[ASN][1000 genomes]
rs6670090	0.83[ASN][1000 genomes]
rs6684929	0.91[EUR][1000 genomes]
rs6687307	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6693179	0.91[EUR][1000 genomes]
rs6698602	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7365290	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7365293	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7368386	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513178	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7513411	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7525346	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7527084	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535319	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6421497	CDCP2	cis	parietal	SCAN
rs6421497	ZYG11B	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56905400-56942600	Weak transcription	Gastric	stomach
2	chr1:56913800-56943200	Weak transcription	Aorta	Aorta
3	chr1:56915200-56935800	Weak transcription	NHLF	lung
4	chr1:56918600-56926600	Weak transcription	Fetal Thymus	thymus
5	chr1:56919200-56927200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:56919200-56930000	Weak transcription	NHDF-Ad	bronchial
7	chr1:56919800-56926600	Weak transcription	Liver	Liver
8	chr1:56919800-56927000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:56919800-56934200	Weak transcription	Fetal Stomach	stomach
10	chr1:56922000-56924400	Enhancers	HUVEC	blood vessel
11	chr1:56922200-56924000	Enhancers	Lung	lung
12	chr1:56922200-56924000	Enhancers	Right Atrium	heart
13	chr1:56922400-56923800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:56922600-56924600	Enhancers	Hela-S3	cervix
15	chr1:56922800-56923800	Weak transcription	Right Ventricle	heart
16	chr1:56922800-56929000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:56922800-56934200	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:56923200-56924000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:56923200-56925000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:56923200-56926200	Weak transcription	HepG2	liver
21	chr1:56923400-56924000	Enhancers	Spleen	Spleen
22	chr1:56923400-56924200	Enhancers	Left Ventricle	heart
23	chr1:56923600-56923800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:56923600-56924000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:56923600-56930000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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