Variant report

Variant	rs6798217
Chromosome Location	chr3:139041241-139041242
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1044826	0.83[MEX][hapmap]
rs10935323	0.87[MEX][hapmap];0.83[MKK][hapmap]
rs12488939	0.87[AMR][1000 genomes]
rs12492883	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12695698	0.83[MEX][hapmap]
rs13083195	0.81[AMR][1000 genomes]
rs3821544	0.83[MEX][hapmap]
rs4383548	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818691	0.87[MEX][hapmap];0.83[MKK][hapmap]
rs9825064	0.87[MEX][hapmap];0.90[MKK][hapmap];0.87[AMR][1000 genomes]
rs9831108	0.83[MEX][hapmap]

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	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6798217	TRPC1	cis	parietal	SCAN
rs6798217	BPESC1	cis	cerebellum	SCAN
rs6798217	KCNK1	trans	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139032400-139048000	Weak transcription	Right Atrium	heart
2	chr3:139037000-139041600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:139037400-139044200	Weak transcription	Pancreas	Pancrea
4	chr3:139037400-139047800	Weak transcription	NHDF-Ad	bronchial
5	chr3:139037800-139047600	Weak transcription	Hela-S3	cervix
6	chr3:139038400-139048000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:139039600-139043400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:139041200-139044800	Weak transcription	K562	blood

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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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