Variant report

Variant	rs1790706
Chromosome Location	chr18:28683238-28683239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:28683155-28683692	HepG2	liver:	n/a	n/a
2	KAP1	chr18:28682213-28683824	U2OS	brain:	n/a	chr18:28683499-28683508 chr18:28683113-28683122
3	JUND	chr18:28682867-28683883	HCT-116	colon:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28683605-28683614
4	FOS	chr18:28682913-28683739	MCF10A-Er-Src	breast:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28683605-28683614
5	FOS	chr18:28682939-28683280	MCF10A-Er-Src	breast:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683110-28683122
6	STAT3	chr18:28682939-28683401	MCF10A-Er-Src	breast:	n/a	chr18:28683172-28683183
7	JUND	chr18:28683073-28683766	HepG2	liver:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28683605-28683614
8	FOS	chr18:28682861-28683673	MCF10A-Er-Src	breast:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28683605-28683614
9	FOSL1	chr18:28682785-28683853	HCT-116	colon:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28683605-28683614
10	STAT3	chr18:28682914-28683269	MCF10A-Er-Src	breast:	n/a	chr18:28683172-28683183
11	POLR2A	chr18:28680002-28683936	K562	blood:	n/a	n/a
12	MYC	chr18:28682815-28683270	MCF10A-Er-Src	breast:	n/a	chr18:28683112-28683121
13	KAP1	chr18:28681981-28683808	HEK293	kidney:	n/a	chr18:28683499-28683508 chr18:28683113-28683122
14	TEAD4	chr18:28682841-28683283	K562	blood:	n/a	n/a
15	FOS	chr18:28682733-28683723	MCF10A-Er-Src	breast:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28683605-28683614
16	MAFK	chr18:28683038-28683613	K562	blood:	n/a	chr18:28683496-28683506 chr18:28683499-28683508
17	CUX1	chr18:28683003-28683669	K562	blood:	n/a	n/a
18	JUND	chr18:28680543-28683681	K562	blood:	n/a	chr18:28683112-28683120 chr18:28683113-28683124 chr18:28683498-28683506 chr18:28683110-28683122 chr18:28683498-28683506 chr18:28683497-28683507 chr18:28683499-28683506 chr18:28683494-28683505 chr18:28681049-28681058 chr18:28683605-28683614
19	MAFF	chr18:28682803-28683643	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:28652105..28654902-chr18:28682018..28683959,2	K562	blood:
2	chr18:28682670..28684930-chr18:28689763..28691596,2	K562	blood:
3	chr18:28682778..28684607-chr18:28773976..28775884,2	MCF-7	breast:

Variant related genes	Relation type
DSC2	TF binding region
ENSG00000238376	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12960042	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1437604	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1595358	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1626413	0.82[EUR][1000 genomes]
rs1626700	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1658108	0.82[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.84[TSI][hapmap]
rs1658110	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1658111	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs1658112	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1658125	0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1658130	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1658135	0.83[EUR][1000 genomes]
rs17800159	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1789036	0.82[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap]
rs1789043	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1789072	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs1790669	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790670	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790671	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790673	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790674	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790675	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2243907	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2577079	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs4799563	0.83[EUR][1000 genomes]
rs4799564	0.82[EUR][1000 genomes]
rs4799565	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388313	chr18:28583296-28693160	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530788	chr18:28596461-28751891	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1790706	CDH2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28682400-28683600	Flanking Active TSS	NHEK	skin
2	chr18:28682600-28683400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:28682600-28683800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:28682600-28684600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr18:28682600-28685400	Weak transcription	Esophagus	oesophagus
6	chr18:28682800-28683400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:28682800-28683600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr18:28682800-28683600	Enhancers	K562	blood
9	chr18:28682800-28684000	Enhancers	HMEC	breast
10	chr18:28682800-28687200	Weak transcription	Stomach Mucosa	stomach
11	chr18:28683000-28683400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr18:28683000-28683400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:28683000-28683800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr18:28683200-28683600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr18:28683200-28683600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr18:28683200-28683800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr18:28683200-28683800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr18:28683200-28683800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr18:28683200-28683800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr18:28683200-28685000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:28683200-28688400	Weak transcription	Fetal Intestine Small	intestine

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