Variant report

Variant	rs853067
Chromosome Location	chr7:80632025-80632026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs701327	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853041	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853042	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs853069	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853070	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853076	0.81[CEU][hapmap]
rs853078	0.81[CEU][hapmap]
rs853086	0.80[EUR][1000 genomes]
rs853092	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1034690	chr7:80520004-80987682	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv888549	chr7:80553950-80652059	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv888550	chr7:80584388-80644661	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv5812	chr7:80601278-80645927	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv521001	chr7:80618038-80644661	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv888551	chr7:80620397-80723062	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs853067	SEMA3C	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80625400-80638200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:80629000-80632800	Weak transcription	Brain Germinal Matrix	brain
3	chr7:80631400-80632600	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:80631800-80632200	Enhancers	Fetal Brain Female	brain
5	chr7:80631800-80632200	Enhancers	Rectal Smooth Muscle	rectum
6	chr7:80631800-80632600	Weak transcription	Fetal Brain Male	brain
7	chr7:80631800-80633600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr7:80632000-80632400	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:80632000-80633000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:80632000-80633000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:80632000-80633200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:80632000-80633200	Weak transcription	Adipose Nuclei	Adipose
13	chr7:80632000-80633200	Weak transcription	HSMM	muscle
14	chr7:80632000-80633200	Weak transcription	NHDF-Ad	bronchial

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Input of quick search could be:

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

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