Variant report

Variant	rs7562741
Chromosome Location	chr2:40102764-40102765
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	chr2:40081608..40083244-chr2:40101423..40104022,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10188106	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11692413	0.88[ASN][1000 genomes]
rs11695763	0.86[ASN][1000 genomes]
rs12475386	0.91[ASN][1000 genomes]
rs13424439	0.91[ASN][1000 genomes]
rs17480505	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1861248	0.91[ASN][1000 genomes]
rs2192703	0.88[ASN][1000 genomes]
rs55768815	0.90[ASN][1000 genomes]
rs60399093	0.89[ASN][1000 genomes]
rs62137179	0.86[ASN][1000 genomes]
rs62137180	0.86[ASN][1000 genomes]
rs62137182	0.88[ASN][1000 genomes]
rs62137183	0.89[ASN][1000 genomes]
rs62137185	0.89[ASN][1000 genomes]
rs62137188	0.99[ASN][1000 genomes]
rs62137214	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556977	0.90[ASN][1000 genomes]
rs887994	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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	nsv1003593	chr2:40009597-40165666	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535651	chr2:40009597-40165666	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv873891	chr2:40046658-40173905	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv430947	chr2:40080723-40141649	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv581496	chr2:40082054-40123904	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873892	chr2:40102764-40139250	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7562741	C2orf56	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40099400-40102800	Weak transcription	HSMM	muscle
2	chr2:40101800-40102800	Weak transcription	NHLF	lung
3	chr2:40102000-40102800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:40102000-40103400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:40102000-40103400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:40102200-40102800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:40102200-40102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:40102200-40103000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:40102400-40102800	Enhancers	Aorta	Aorta
10	chr2:40102400-40102800	Enhancers	Fetal Stomach	stomach
11	chr2:40102400-40103000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:40102400-40103000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:40102400-40103000	Enhancers	Fetal Muscle Leg	muscle
14	chr2:40102400-40103000	Enhancers	NHEK	skin
15	chr2:40102400-40103200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:40102400-40103200	Enhancers	Brain Anterior Caudate	brain
17	chr2:40102400-40103200	Enhancers	NH-A	brain
18	chr2:40102400-40103400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:40102400-40103400	Enhancers	Ovary	ovary
20	chr2:40102400-40103400	Enhancers	A549	lung
21	chr2:40102400-40103400	Enhancers	HMEC	breast
22	chr2:40102400-40103400	Enhancers	Osteobl	bone
23	chr2:40102400-40103600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:40102400-40103600	Enhancers	Colon Smooth Muscle	Colon
25	chr2:40102600-40103000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:40102600-40103200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:40102600-40103200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:40102600-40103200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr2:40102600-40103400	Enhancers	Adipose Nuclei	Adipose
30	chr2:40102600-40103400	Enhancers	NHDF-Ad	bronchial

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