Variant report

Variant	rs1992643
Chromosome Location	chr1:212455024-212455025
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	FOS	chr1:212454974-212455279	MCF10A-Er-Src	breast:	n/a	chr1:212455080-212455089
2	MYC	chr1:212454973-212455253	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:212455011-212455180	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:212454875-212455322	IMR90	lung:	n/a	chr1:212455125-212455136
5	CEBPB	chr1:212454944-212455267	A549	lung:	n/a	chr1:212455125-212455136
6	CEBPB	chr1:212454913-212455300	Hela-S3	cervix:	n/a	chr1:212455125-212455136
7	FOS	chr1:212454971-212455294	MCF10A-Er-Src	breast:	n/a	chr1:212455080-212455089
8	CEBPB	chr1:212454949-212455285	HepG2	liver:	n/a	chr1:212455125-212455136
9	MAFK	chr1:212455015-212455224	IMR90	lung:	n/a	n/a
10	MYC	chr1:212455001-212455279	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr1:212454989-212455263	H1-hESC	embryonic stem cell:	n/a	chr1:212455125-212455136
12	JUND	chr1:212454977-212455160	HepG2	liver:	n/a	chr1:212455080-212455089
13	FOS	chr1:212454989-212455274	MCF10A-Er-Src	breast:	n/a	chr1:212455080-212455089
14	CEBPB	chr1:212454918-212455245	ECC-1	luminal epithelium:	n/a	chr1:212455125-212455136
15	FOS	chr1:212455005-212455278	MCF10A-Er-Src	breast:	n/a	chr1:212455080-212455089
16	CEBPB	chr1:212454932-212455294	ECC-1	luminal epithelium:	n/a	chr1:212455125-212455136
17	CEBPB	chr1:212454952-212455303	K562	blood:	n/a	chr1:212455125-212455136

Variant related genes	Relation type
PPP2R5A	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10019	0.96[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11119904	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12023488	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12033246	0.96[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12035647	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12036130	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389371	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs17042034	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1774249	0.92[CEU][hapmap];0.93[CHB][hapmap]
rs2252044	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2298114	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs2516331	0.84[EUR][1000 genomes]
rs2589474	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3099112	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[EUR][1000 genomes]
rs351373	0.84[EUR][1000 genomes]
rs351377	0.84[EUR][1000 genomes]
rs351378	0.84[EUR][1000 genomes]
rs351379	0.84[EUR][1000 genomes]
rs351380	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs351386	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs351393	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs351398	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs351401	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351407	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs351408	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs351417	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs351419	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3767861	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3767862	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3767863	0.82[EUR][1000 genomes]
rs4951582	0.84[EUR][1000 genomes]
rs4951588	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs4951589	0.96[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6659594	0.82[EUR][1000 genomes]
rs7415843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7519959	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7544225	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs792445	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1992643	NENF	cis	Esophagus Mucosa	GTEx
rs1992643	TMEM206	cis	Esophagus Mucosa	GTEx
rs1992643	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212446000-212457000	Weak transcription	Stomach Mucosa	stomach
2	chr1:212446000-212457600	Weak transcription	Fetal Brain Female	brain
3	chr1:212446400-212457200	Weak transcription	Fetal Heart	heart
4	chr1:212454200-212457200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:212454600-212455400	Enhancers	Fetal Lung	lung
6	chr1:212455000-212455200	Enhancers	Hela-S3	cervix
7	chr1:212455000-212455200	Enhancers	NHLF	lung
8	chr1:212455000-212455400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr1:212455000-212455400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:212455000-212455400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:212455000-212455800	Enhancers	NHDF-Ad	bronchial

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