Variant report

Variant	rs2378425
Chromosome Location	chr1:221016058-221016059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10495152	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863567	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863568	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118609	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118611	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118615	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118616	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11118619	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590678	0.80[ASN][1000 genomes]
rs12057411	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12073837	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12089958	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12117818	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12123589	0.95[AFR][1000 genomes]
rs12124030	0.80[ASN][1000 genomes]
rs12129004	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12139139	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12145674	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335919	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1494368	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1494371	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494372	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17008806	0.89[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs17596850	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17650107	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242358	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs2279638	0.94[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2642421	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs35730037	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4143773	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61830270	0.86[ASN][1000 genomes]
rs61830289	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541161	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6668666	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6673877	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693017	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7530074	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530176	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7530493	0.94[ASN][1000 genomes]
rs7544735	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553447	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs881995	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs903319	0.89[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs984676	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2378425	C1orf115	cis	cerebellum	SCAN
rs2378425	BPNT1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221002800-221016200	Weak transcription	Fetal Lung	lung
2	chr1:221013400-221017200	Weak transcription	Right Atrium	heart
3	chr1:221013400-221018000	Weak transcription	Right Ventricle	heart
4	chr1:221015200-221016800	Enhancers	HUVEC	blood vessel
5	chr1:221015400-221018200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:221015600-221016400	Enhancers	Fetal Kidney	kidney
7	chr1:221015600-221017400	Enhancers	Fetal Muscle Leg	muscle
8	chr1:221015600-221017400	Enhancers	Left Ventricle	heart
9	chr1:221015600-221017600	Enhancers	Colon Smooth Muscle	Colon
10	chr1:221015600-221018200	Enhancers	Fetal Stomach	stomach
11	chr1:221015600-221018400	Enhancers	Fetal Heart	heart
12	chr1:221015800-221017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:221015800-221017400	Enhancers	Adipose Nuclei	Adipose
14	chr1:221016000-221017000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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