Variant report

Variant	rs9807610
Chromosome Location	chr18:9620202-9620203
allele	C/T
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	HDAC2	chr18:9620132-9620347	K562	blood:	n/a	n/a
2	ZNF384	chr18:9619947-9620384	K562	blood:	n/a	n/a
3	CEBPB	chr18:9620096-9620314	H1-hESC	embryonic stem cell:	n/a	chr18:9620226-9620237
4	CEBPB	chr18:9619958-9620303	K562	blood:	n/a	chr18:9620226-9620237
5	CEBPB	chr18:9620050-9620426	HepG2	liver:	n/a	chr18:9620226-9620237
6	CEBPB	chr18:9620166-9620279	HepG2	liver:	n/a	chr18:9620226-9620237
7	CEBPB	chr18:9620049-9620386	K562	blood:	n/a	chr18:9620226-9620237
8	CEBPB	chr18:9619999-9620321	A549	lung:	n/a	chr18:9620226-9620237
9	CEBPB	chr18:9620051-9620417	A549	lung:	n/a	chr18:9620226-9620237
10	CEBPB	chr18:9619429-9620429	IMR90	lung:	n/a	chr18:9620226-9620237
11	CEBPB	chr18:9620157-9620320	MCF-7	breast:	n/a	chr18:9620226-9620237
12	RCOR1	chr18:9619631-9620436	K562	blood:	n/a	n/a
13	CEBPB	chr18:9619942-9620341	A549	lung:	n/a	chr18:9620226-9620237
14	CEBPB	chr18:9620049-9620425	Hela-S3	cervix:	n/a	chr18:9620226-9620237
15	HDAC2	chr18:9619984-9620340	K562	blood:	n/a	n/a
16	CEBPB	chr18:9620110-9620316	K562	blood:	n/a	chr18:9620226-9620237
17	RCOR1	chr18:9620065-9620437	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9612628..9617891-chr18:9619605..9623342,5	MCF-7	breast:
2	chr18:9614482..9616420-chr18:9617986..9621274,5	K562	blood:

Variant related genes	Relation type
PPP4R1	TF binding region
RNU6-903P	TF binding region
ENSG00000263627	Chromatin interaction
ENSG00000154845	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1662885	0.86[ASN][1000 genomes]
rs1787165	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1787166	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028661	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028662	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2028663	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2289684	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35444634	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs428598	0.82[EUR][1000 genomes]
rs583306	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs589559	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62088920	0.89[AMR][1000 genomes]
rs638578	0.86[ASN][1000 genomes]
rs667695	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs671339	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs677461	0.81[ASN][1000 genomes]
rs680478	0.83[EUR][1000 genomes]
rs681297	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs694861	0.86[ASN][1000 genomes]
rs7234128	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7359735	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8088389	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8090919	0.86[ASN][1000 genomes]
rs9807577	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9807604	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9807614	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9950583	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv1820504	chr18:9614250-9621841	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1801741	chr18:9614451-9621841	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv521175	chr18:9615851-9623052	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9807610	RP11-692N5.1	cis	Esophagus Mucosa	GTEx
rs9807610	RP11-692N5.1	cis	Nerve Tibial	GTEx
rs9807610	RP11-692N5.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9807610	RP11-692N5.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9615800-9625200	Weak transcription	Placenta	Placenta
2	chr18:9615800-9625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr18:9615800-9627400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:9617400-9625400	Weak transcription	HMEC	breast
5	chr18:9617600-9630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:9619600-9620400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr18:9619800-9627400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr18:9620000-9625400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr18:9620000-9625600	Weak transcription	Hela-S3	cervix
10	chr18:9620000-9627200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr18:9620000-9627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr18:9620000-9627600	Weak transcription	NHDF-Ad	bronchial
13	chr18:9620200-9621400	Enhancers	HUVEC	blood vessel
14	chr18:9620200-9623800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr18:9620200-9625200	Weak transcription	NHEK	skin
16	chr18:9620200-9625400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr18:9620200-9625600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr18:9620200-9627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr18:9620200-9627400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr18:9620200-9627400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr18:9620200-9627400	Weak transcription	NHLF	lung
22	chr18:9620200-9627400	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links