Variant report

Variant	rs2256602
Chromosome Location	chr2:145792165-145792166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12691702	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13386034	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1371045	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1438895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528412	0.80[ASN][1000 genomes]
rs1837294	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1898731	0.82[JPT][hapmap]
rs2246363	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2950790	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3901734	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv834398	chr2:145659419-145830156	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv431768	chr2:145741527-145981491	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2256602	KIAA0664L3	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145786000-145793600	Weak transcription	HSMMtube	muscle
2	chr2:145787800-145794600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:145788000-145793800	Weak transcription	Brain Anterior Caudate	brain
4	chr2:145788000-145793800	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:145788000-145794000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:145788000-145794000	Weak transcription	Brain Substantia Nigra	brain
7	chr2:145788800-145792200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:145788800-145793000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:145788800-145793200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:145789200-145792200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:145789200-145793400	Weak transcription	Osteobl	bone
12	chr2:145789200-145793800	Weak transcription	Ovary	ovary
13	chr2:145789200-145802400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:145789800-145794200	Weak transcription	Fetal Lung	lung
15	chr2:145791200-145792400	Weak transcription	A549	lung
16	chr2:145791400-145792200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:145791400-145792400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:145792000-145792800	Enhancers	NHDF-Ad	bronchial

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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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