Variant report

Variant	rs12542601
Chromosome Location	chr8:61166119-61166120
allele	A/G
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:15)

rs_ID	r²[population]
rs10092218	0.86[JPT][hapmap]
rs12543911	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12708003	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13248852	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13271624	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16926002	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16926008	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1893275	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs35323112	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59550103	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73250004	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7461425	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7464602	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7824479	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs899741	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
2	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv831333	chr8:61102862-61275122	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv890943	chr8:61134995-61225652	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12542601	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61117800-61167400	Weak transcription	Fetal Stomach	stomach
2	chr8:61158600-61166200	Weak transcription	Gastric	stomach
3	chr8:61158600-61174600	Weak transcription	Fetal Intestine Large	intestine
4	chr8:61158800-61176800	Weak transcription	A549	lung
5	chr8:61159200-61166800	Weak transcription	Left Ventricle	heart
6	chr8:61161000-61166600	Weak transcription	Fetal Kidney	kidney
7	chr8:61162000-61170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:61164000-61171800	Strong transcription	K562	blood
9	chr8:61164200-61186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:61164600-61169400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:61165600-61167400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr8:61166000-61167400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr8:61166000-61167600	Enhancers	Primary hematopoietic stem cells	blood
14	chr8:61166000-61169000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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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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