Variant report

Variant	rs12577167
Chromosome Location	chr11:5475118-5475119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:4988858-5002113..11:5469844-5475173	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000225003	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10838132	0.85[CHB][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap]
rs10838150	0.85[CHB][hapmap]
rs11037489	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11037531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11037542	0.85[YRI][hapmap]
rs11037558	0.85[CHB][hapmap]
rs11037559	0.81[CHB][hapmap]
rs11037561	0.85[CHB][hapmap]
rs1118716	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12278135	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs12576842	1.00[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12577995	0.84[CHB][hapmap]
rs1368691	0.84[CHB][hapmap]
rs1391618	0.84[CHB][hapmap]
rs16926541	0.85[CHB][hapmap];0.85[YRI][hapmap]
rs16931671	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs2467217	0.85[CHB][hapmap]
rs2471988	0.85[CHB][hapmap]
rs2471989	0.83[CHB][hapmap]
rs2736577	0.84[CHB][hapmap]
rs2736578	0.85[CHB][hapmap]
rs61892073	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7106350	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs7932643	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
2	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv430314	chr11:5411744-5496924	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	esv2757420	chr11:5416622-5492033	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	esv2759800	chr11:5416622-5492033	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
8	nsv896935	chr11:5427118-5490077	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
9	nsv896937	chr11:5427118-5493309	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	nsv896936	chr11:5427118-5493370	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	esv34391	chr11:5431984-5493309	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
12	nsv1050290	chr11:5440287-5497617	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv1046764	chr11:5442226-5497617	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
14	nsv1039047	chr11:5461214-5497617	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
15	esv2761647	chr11:5472735-5480645	Enhancers Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12577167	CNGA4	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5465800-5481800	Strong transcription	K562	blood
2	chr11:5474800-5475600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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