Variant report

Variant	rs4662402
Chromosome Location	chr2:145644545-145644546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10928231	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10928232	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11674165	0.88[EUR][1000 genomes]
rs11677125	0.81[ASN][1000 genomes]
rs11677207	0.81[ASN][1000 genomes]
rs11677298	0.81[ASN][1000 genomes]
rs12151653	0.88[EUR][1000 genomes]
rs1438896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17479393	0.95[ASN][1000 genomes]
rs1918877	0.84[ASN][1000 genomes]
rs2077917	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs6738560	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72854449	0.91[EUR][1000 genomes]
rs72854464	0.88[EUR][1000 genomes]
rs7571520	0.84[ASN][1000 genomes]
rs7603126	0.82[ASN][1000 genomes]
rs7603230	0.82[ASN][1000 genomes]
rs9646682	0.95[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002563	chr2:145182201-145863253	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv535957	chr2:145182201-145863253	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv932113	chr2:145515124-145844491	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4662402	KIAA0664L3	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145644400-145644600	Enhancers	Fetal Lung	lung
2	chr2:145644400-145644800	Enhancers	Brain Cingulate Gyrus	brain
3	chr2:145644400-145644800	Enhancers	Brain Hippocampus Middle	brain
4	chr2:145644400-145644800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:145644400-145644800	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:145644400-145645200	Enhancers	Adipose Nuclei	Adipose
7	chr2:145644400-145645200	Enhancers	Fetal Muscle Trunk	muscle
8	chr2:145644400-145645200	Enhancers	Fetal Muscle Leg	muscle
9	chr2:145644400-145645400	Enhancers	Left Ventricle	heart
10	chr2:145644400-145645400	Enhancers	Ovary	ovary
11	chr2:145644400-145645400	Enhancers	Psoas Muscle	Psoas
12	chr2:145644400-145645600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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