Variant report

Variant	rs7619876
Chromosome Location	chr3:112864351-112864352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16860564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860599	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs1881941	0.81[ASN][1000 genomes]
rs1881945	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs1920079	0.93[ASN][1000 genomes]
rs1920081	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs28671320	0.88[ASN][1000 genomes]
rs55705442	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62264167	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223921	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630958	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9822730	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9824380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830821	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7619876	ATP6V1A	cis	cerebellum	SCAN
rs7619876	TAGLN3	cis	cerebellum	SCAN
rs7619876	CD96	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112847800-112866800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112849400-112865200	Weak transcription	Fetal Stomach	stomach
3	chr3:112852800-112866800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:112855000-112866800	Weak transcription	Pancreas	Pancrea
5	chr3:112858600-112867400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:112862000-112864400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:112862400-112864400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:112862600-112866200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:112862600-112866600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:112862600-112866800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:112862600-112866800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:112862800-112866000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:112862800-112866400	Weak transcription	NHEK	skin
14	chr3:112862800-112866800	Weak transcription	HMEC	breast
15	chr3:112863000-112866400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:112863200-112866800	Weak transcription	Esophagus	oesophagus
17	chr3:112863400-112864600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:112863400-112870600	Weak transcription	Left Ventricle	heart
19	chr3:112864000-112865600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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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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