Variant report

Variant	rs489964
Chromosome Location	chr15:43517554-43517555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:43517541-43518067	GM12878	blood:	n/a	n/a
2	CTCF	chr15:43517499-43518034	HCT-116	colon:	n/a	n/a
3	CTCF	chr15:43517527-43518142	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr15:43517383-43518040	A549	lung:	n/a	n/a
5	CTCF	chr15:43517546-43517992	HCT-116	colon:	n/a	n/a
6	RAD21	chr15:43517548-43518128	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr15:43517420-43517570	GM12872	blood:	n/a	n/a
8	CTCF	chr15:43517534-43518045	K562	blood:	n/a	n/a
9	RAD21	chr15:43517344-43518128	SK-N-SH	brain:	n/a	n/a
10	SMC3	chr15:43517484-43518057	SK-N-SH	brain:	n/a	n/a
11	RAD21	chr15:43517505-43518088	HCT-116	colon:	n/a	n/a
12	RAD21	chr15:43517546-43518056	ECC-1	luminal epithelium:	n/a	n/a
13	RAD21	chr15:43517554-43518043	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:43517383..43518225-chr15:43577794..43578313,2	MCF-7	breast:
2	chr15:43517369..43518401-chr15:43577428..43578017,4	K562	blood:
3	chr15:43511739..43513912-chr15:43515291..43517866,3	K562	blood:
4	chr15:43517417..43518218-chr15:43560788..43561555,3	MCF-7	breast:
5	chr1:200167551..200168288-chr15:43517032..43517929,2	MCF-7	breast:
6	chr15:43517344..43517927-chr15:43574420..43575212,2	K562	blood:
7	chr15:43517345..43518266-chr15:43560680..43561199,2	K562	blood:
8	chr15:43500895..43501461-chr15:43517373..43518252,2	MCF-7	breast:

No data

Variant related genes	Relation type
EPB42	TF binding region
ENSG00000166947	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10851414	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070389	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs11070390	0.85[ASN][1000 genomes]
rs11632120	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12442190	0.88[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs12913112	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12913134	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1474200	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1814323	1.00[ASW][hapmap]
rs2056346	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2139651	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs2139652	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2438149	0.87[AFR][1000 genomes]
rs476342	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923956	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs502157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504417	1.00[ASW][hapmap]
rs513970	1.00[ASW][hapmap]
rs525403	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs530118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs531598	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574856	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165861	0.83[ASN][1000 genomes]
rs7166467	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs489964	CD40	trans	cerebellum	SCAN
rs489964	TGM5	cis	lymphoblastoid	seeQTL
rs489964	LIMA1	trans	lymphoblastoid	seeQTL
rs489964	WDR76	cis	parietal	SCAN
rs489964	SNAP23	cis	cerebellum	SCAN
rs489964	CCNDBP1	cis	multi-tissue	Pritchard
rs489964	TYRO3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43506400-43518600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43511800-43526600	Weak transcription	Esophagus	oesophagus
3	chr15:43512600-43517800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:43513400-43517600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:43514000-43517600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:43514000-43522600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:43515000-43517600	Weak transcription	K562	blood

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