Variant report

Variant	rs4672097
Chromosome Location	chr2:56430903-56430904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1159916	0.81[CHD][hapmap]
rs12620171	0.93[EUR][1000 genomes]
rs17190072	0.88[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17268702	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1814277	0.80[CEU][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs1861772	0.83[MKK][hapmap]
rs2193478	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2216326	0.92[ASN][1000 genomes]
rs4140787	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4671277	0.90[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs4672098	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[EUR][1000 genomes]
rs4672099	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[EUR][1000 genomes]
rs56399326	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6754349	0.86[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72801175	0.93[ASN][1000 genomes]
rs8179803	0.90[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised 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 miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4672097	CCDC85A	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56414000-56434000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:56420600-56443200	Weak transcription	Adipose Nuclei	Adipose
3	chr2:56421200-56437200	Weak transcription	Left Ventricle	heart
4	chr2:56423000-56443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:56423200-56434600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:56427800-56431600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:56429400-56431000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:56429400-56437200	Strong transcription	HSMM	muscle
9	chr2:56429600-56431000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:56429800-56433200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:56430400-56436000	Weak transcription	Fetal Brain Male	brain
12	chr2:56430600-56434400	Weak transcription	HUVEC	blood vessel
13	chr2:56430800-56431600	Enhancers	HMEC	breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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