Variant report

Variant	rs7652623
Chromosome Location	chr3:139817289-139817290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16849851	0.87[CHB][hapmap]
rs1878978	0.87[CHB][hapmap]
rs2350488	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[LWK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4368461	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs4683797	0.82[CHB][hapmap]

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	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv877545	chr3:139738645-139821310	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv829739	chr3:139797496-140002685	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7652623	COPB2	cis	parietal	SCAN
rs7652623	CHST2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139812600-139819600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:139812600-139820400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:139813200-139817600	Weak transcription	Fetal Brain Male	brain
4	chr3:139813200-139817600	Weak transcription	Fetal Brain Female	brain
5	chr3:139813800-139832600	Weak transcription	Ovary	ovary
6	chr3:139815600-139822000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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