Variant report

Variant	rs6531976
Chromosome Location	chr4:88241220-88241221
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs58693841	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58852125	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59971263	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6531974	0.84[YRI][hapmap]
rs6828094	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6828253	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6833257	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6840298	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839194	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73841129	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7676494	0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs7678047	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7682602	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv879527	chr4:88194170-88250203	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv1802846	chr4:88211056-88246450	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv293508	chr4:88238744-88241534	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88229000-88245000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:88235200-88243800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:88235600-88241400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:88235800-88242600	Weak transcription	Adipose Nuclei	Adipose
5	chr4:88236800-88243200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:88238600-88253400	Weak transcription	HepG2	liver
7	chr4:88239400-88248000	Weak transcription	Fetal Intestine Small	intestine
8	chr4:88239400-88255400	Weak transcription	A549	lung
9	chr4:88241000-88244200	Active TSS	Liver	Liver

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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