Variant report

Variant	rs840163
Chromosome Location	chr12:57320711-57320712
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57319135..57322195-chr12:57322954..57326796,4	K562	blood:
2	chr12:57155856..57157540-chr12:57319760..57321568,2	MCF-7	breast:
3	chr12:57117768..57120708-chr12:57319808..57322121,2	MCF-7	breast:
4	chr12:57320297..57321910-chr12:57382955..57384633,2	MCF-7	breast:
5	chr12:57315576..57318465-chr12:57319444..57323573,6	MCF-7	breast:
6	chr12:57319841..57322040-chr12:57335776..57337907,3	MCF-7	breast:
7	chr12:57319668..57321739-chr12:57328699..57331375,2	MCF-7	breast:
8	chr12:57232523..57234649-chr12:57320169..57322431,2	MCF-7	breast:
9	chr12:57319872..57321581-chr12:57347777..57350711,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196531	Chromatin interaction
ENSG00000025423	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1072669	0.82[JPT][hapmap];0.85[MEX][hapmap]
rs11172071	0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs11172072	0.82[ASN][1000 genomes]
rs1601405	0.82[JPT][hapmap];0.85[MEX][hapmap]
rs17119173	0.82[JPT][hapmap]
rs1872436	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2629413	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3782331	0.82[JPT][hapmap]
rs719749	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs719750	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7314055	0.83[GIH][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.87[ASN][1000 genomes]
rs7314151	0.83[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs7314262	0.82[JPT][hapmap];0.85[MEX][hapmap]
rs7970701	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs840160	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs840162	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844469	0.88[JPT][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs863459	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs864541	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs901069	0.82[JPT][hapmap];0.85[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv899107	chr12:57293436-57321212	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv438213	chr12:57319810-57324496	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs840163	KRT82	cis	parietal	SCAN
rs840163	OR6C1	cis	cerebellum	SCAN
rs840163	MYL6	cis	parietal	SCAN
rs840163	RDH5	cis	parietal	SCAN
rs840163	NCKAP1L	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57316200-57321400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:57316400-57326800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:57317400-57323400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:57317600-57323000	Weak transcription	Esophagus	oesophagus

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