Variant report

Variant	rs7980357
Chromosome Location	chr12:105840226-105840227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105837457..105842094-chr12:106531449..106535531,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074590	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10746030	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10746031	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10746032	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10746033	0.88[ASN][1000 genomes]
rs10778399	0.86[ASN][1000 genomes]
rs10778400	0.87[ASN][1000 genomes]
rs10778401	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10778404	0.92[ASN][1000 genomes]
rs10778405	0.92[ASN][1000 genomes]
rs10861425	0.87[ASN][1000 genomes]
rs10861427	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861428	0.97[ASN][1000 genomes]
rs11112529	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1821231	0.84[ASN][1000 genomes]
rs2060203	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2103230	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964136	0.86[ASN][1000 genomes]
rs4964139	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964373	0.86[ASN][1000 genomes]
rs4964376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311949	0.92[ASN][1000 genomes]
rs934415	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs934416	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9788109	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788271	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	nsv899501	chr12:105819046-105950801	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv832507	chr12:105821685-106005186	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1045689	chr12:105836970-105879110	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7980357	ANO4	cis	parietal	SCAN
rs7980357	RIC8B	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105836600-105840600	Enhancers	HSMMtube	muscle
2	chr12:105837000-105840400	Enhancers	HSMM	muscle
3	chr12:105837400-105840400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:105837400-105840600	Enhancers	HUVEC	blood vessel
5	chr12:105837600-105840400	Enhancers	NHEK	skin
6	chr12:105837800-105840400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:105838200-105840400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:105838200-105840400	Enhancers	HMEC	breast
9	chr12:105838200-105845400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:105838400-105840400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:105838600-105841400	Enhancers	Hela-S3	cervix
12	chr12:105840000-105840600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:105840000-105841000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:105840000-105841200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:105840000-105843200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:105840000-105846400	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:105840200-105840400	Enhancers	Adipose Nuclei	Adipose
18	chr12:105840200-105844600	Weak transcription	Muscle Satellite Cultured Cells	--

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