Variant report

Variant	rs4964423
Chromosome Location	chr12:106254333-106254334
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:106246232..106247758-chr12:106252857..106254450,2	MCF-7	breast:
2	chr12:106135266..106136098-chr12:106254116..106254831,3	MCF-7	breast:
3	chr12:106252576..106257330-chr12:106324880..106330173,10	MCF-7	breast:
4	chr12:106252439..106256460-chr12:106528954..106534113,10	MCF-7	breast:
5	chr12:106248554..106253147-chr12:106253796..106257710,5	MCF-7	breast:
6	chr12:106126183..106128065-chr12:106252083..106254658,2	MCF-7	breast:
7	chr12:106252103..106254778-chr12:106324324..106327304,2	MCF-7	breast:
8	chr12:106253022..106256354-chr12:106530460..106534147,5	MCF-7	breast:
9	chr12:105837444..105839027-chr12:106252891..106255471,2	MCF-7	breast:
10	chr12:106169085..106169798-chr12:106254145..106255071,2	MCF-7	breast:
11	chr12:106253691..106256253-chr12:106286526..106288300,2	MCF-7	breast:
12	chr12:106233406..106235430-chr12:106254308..106256994,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10746051	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10861524	0.86[ASN][1000 genomes]
rs10861525	0.86[ASN][1000 genomes]
rs10861532	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1421442	0.91[AMR][1000 genomes]
rs1862033	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2374558	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4964169	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4964426	0.81[AMR][1000 genomes]
rs7955669	0.82[YRI][hapmap]
rs7972359	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4964423	CCDC53	cis	cerebellum	SCAN
rs4964423	CCDC53	cis	parietal	SCAN
rs4964423	CHPT1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106249400-106256800	Weak transcription	HSMMtube	muscle
2	chr12:106249800-106255000	Weak transcription	Left Ventricle	heart

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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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