Variant report

Variant	rs3003377
Chromosome Location	chr1:10060516-10060517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10779734	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11121510	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11121512	0.85[ASN][1000 genomes]
rs12140058	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1220400	0.81[ASN][1000 genomes]
rs1220402	0.83[ASN][1000 genomes]
rs1220420	0.81[ASN][1000 genomes]
rs1220421	0.81[ASN][1000 genomes]
rs1220424	0.83[ASN][1000 genomes]
rs1234694	0.80[ASN][1000 genomes]
rs1660733	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2890358	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3003376	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3003378	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3013788	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3123522	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs58528460	0.81[AFR][1000 genomes]
rs6541073	0.83[ASN][1000 genomes]
rs6661806	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6664631	0.87[ASN][1000 genomes]
rs6678023	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680076	0.81[ASN][1000 genomes]
rs7517360	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7517806	0.82[ASN][1000 genomes]
rs7517812	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7539191	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3003377	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10058200-10061000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:10058400-10060800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:10058400-10061000	Weak transcription	Brain Anterior Caudate	brain
4	chr1:10058400-10061200	Weak transcription	Esophagus	oesophagus
5	chr1:10059200-10061200	Active TSS	Adipose Nuclei	Adipose
6	chr1:10059200-10075000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links