Variant report

Variant	rs6749322
Chromosome Location	chr2:55167820-55167821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10211316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3821112	0.84[AFR][1000 genomes]
rs6744548	0.93[LWK][hapmap]
rs6759673	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7355428	0.86[GIH][hapmap]
rs7586885	0.95[LWK][hapmap];0.89[YRI][hapmap]
rs7589959	0.86[LWK][hapmap];0.89[YRI][hapmap]
rs7590241	0.89[YRI][hapmap]
rs7590265	0.93[LWK][hapmap];0.89[YRI][hapmap]
rs7600676	0.95[LWK][hapmap];0.89[YRI][hapmap]

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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6749322	GTF2E2	trans	parietal	SCAN
rs6749322	CCDC85A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55150000-55168400	Weak transcription	Pancreas	Pancrea
2	chr2:55154400-55168000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:55165800-55169200	Enhancers	Fetal Muscle Leg	muscle
4	chr2:55166200-55169000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:55166200-55172800	Weak transcription	Gastric	stomach
6	chr2:55167000-55168400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:55167600-55168400	Enhancers	Brain Anterior Caudate	brain
8	chr2:55167600-55168400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:55167600-55169000	Enhancers	HepG2	liver
10	chr2:55167800-55168600	Enhancers	Brain Substantia Nigra	brain
11	chr2:55167800-55169000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55167800-55169000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:55167800-55169800	Enhancers	Brain Hippocampus Middle	brain
14	chr2:55167800-55170000	Enhancers	Brain Angular Gyrus	brain

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Input of quick search could be:

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

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