Variant report

Variant	rs2939817
Chromosome Location	chr12:58517000-58517001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58516937..58519947-chr17:41380326..41383375,3	K562	blood:
2	chr12:58516945..58519917-chr17:41466381..41467898,2	K562	blood:
3	chr12:58516937..58518437-chr17:41400928..41402668,2	MCF-7	breast:
4	chr12:58516917..58519927-chr17:41462306..41466299,7	K562	blood:
5	chr12:58516917..58519917-chr3:73158604..73161610,3	K562	blood:
6	chr11:62607619..62609220-chr12:58516927..58518437,3	MCF-7	breast:
7	chr12:58516925..58518425-chr17:41438461..41440788,2	MCF-7	breast:
8	chr12:58516917..58519927-chr17:41462306..41466156,7	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000223247	Chromatin interaction
ENSG00000236383	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000188825	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10877071	0.80[EUR][1000 genomes]
rs2088987	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60819865	0.80[EUR][1000 genomes]
rs7956463	0.97[EUR][1000 genomes];0.93[ASN][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	nsv899124	chr12:58391839-58883507	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv729	chr12:58490094-58535466	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3332556	chr12:58499734-58525494	Enhancers Active TSS Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
4	esv3367170	chr12:58500734-58523126	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	esv2760247	chr12:58516781-58525282	Weak transcription Active TSS Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2939817	XRCC6BP1	cis	multi-tissue	Pritchard
rs2939817	XRCC6BP1	cis	Artery Tibial	GTEx
rs2939817	OR6C65	cis	parietal	SCAN
rs2939817	HOXC6	cis	parietal	SCAN
rs2939817	OR6C2	cis	cerebellum	SCAN
rs2939817	MOBKL2C	trans	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58514000-58517000	Weak transcription	Ovary	ovary
2	chr12:58514200-58517000	Weak transcription	Psoas Muscle	Psoas
3	chr12:58517000-58517400	Active TSS	Ovary	ovary

Quick Search:

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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