Variant report

Variant	rs4140501
Chromosome Location	chr22:32676841-32676842
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:32170492-32188129..22:32670527-32676849	Hela-S3	cervix:
2	22:32012966-32043914..22:32670527-32676849	K562	blood:
3	22:32670527-32676849..22:32920308-32927723	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000100150	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12168999	0.96[CEU][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2005955	0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2049911	0.96[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413102	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2899182	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820072	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4821046	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4821052	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4821053	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4821055	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5749366	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5749370	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749376	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5749385	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5749386	0.84[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753914	0.86[AFR][1000 genomes]
rs5753935	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753937	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753946	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753965	0.80[AMR][1000 genomes]
rs5994525	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv2830423	chr22:32477718-32767825	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv2422247	chr22:32486448-32788258	Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	nsv834178	chr22:32490449-32677521	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	esv2753006	chr22:32592120-32719481	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv979756	chr22:32669633-32681470	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4140501	NF2	cis	parietal	SCAN
rs4140501	AP1B1	cis	parietal	SCAN
rs4140501	CHEK2	cis	cerebellum	SCAN
rs4140501	C22orf28	cis	parietal	SCAN
rs4140501	SEC14L3	cis	parietal	SCAN
rs4140501	RASL10A	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32674000-32690000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr22:32676200-32677800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr22:32676400-32677200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
4	chr22:32676400-32677400	Enhancers	Brain Cingulate Gyrus	brain
5	chr22:32676400-32677600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:32676400-32677800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:32676400-32677800	Enhancers	HMEC	breast
8	chr22:32676600-32677000	Enhancers	Brain Angular Gyrus	brain
9	chr22:32676600-32677000	Enhancers	Brain Hippocampus Middle	brain
10	chr22:32676800-32677000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr22:32676800-32677000	Enhancers	Fetal Brain Female	brain
12	chr22:32676800-32677000	Flanking Active TSS	NHEK	skin
13	chr22:32676800-32677200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr22:32676800-32677200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:32676800-32677400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:32676800-32677400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:32676800-32677400	Enhancers	Brain Germinal Matrix	brain
18	chr22:32676800-32677400	Enhancers	NH-A	brain

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