Variant report

Variant	rs3925518
Chromosome Location	chr5:178072229-178072230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178051814..178054054-chr5:178071532..178073696,2	MCF-7	breast:
2	chr5:178063341..178065728-chr5:178071679..178073201,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10063148	0.92[CEU][hapmap]
rs10063220	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479500	0.84[CEU][hapmap]
rs11249556	0.82[ASN][1000 genomes]
rs11737903	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11740194	0.83[ASN][1000 genomes]
rs11746942	0.83[ASN][1000 genomes]
rs11747742	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs12188543	0.82[CEU][hapmap]
rs12189095	0.82[CEU][hapmap]
rs12514311	0.85[ASN][1000 genomes]
rs12518589	0.91[ASN][1000 genomes]
rs13156622	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs262027	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs35522922	0.89[ASN][1000 genomes]
rs36008351	0.91[ASN][1000 genomes]
rs3925517	0.82[CEU][hapmap]
rs4079110	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4587090	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976738	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4976800	0.82[ASN][1000 genomes]
rs530542	0.82[ASN][1000 genomes]
rs596780	0.88[CHD][hapmap]
rs602451	0.88[CHD][hapmap]
rs628857	0.89[JPT][hapmap]
rs643936	0.83[ASN][1000 genomes]
rs6863876	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6865775	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882079	0.83[ASN][1000 genomes]
rs6883747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890632	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702727	0.83[ASN][1000 genomes]
rs9329045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329046	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1023697	chr5:178070594-178126328	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv537972	chr5:178070594-178126328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3925518	MAML1	cis	cerebellum	SCAN
rs3925518	CLK4	Cis_1M	lymphoblastoid	RTeQTL
rs3925518	PROP1	cis	cerebellum	SCAN
rs3925518	CLK4	cis	cerebellum	SCAN
rs3925518	RUFY1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178067600-178072400	Enhancers	Osteobl	bone
2	chr5:178070200-178078000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:178071200-178072600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:178071200-178072600	Enhancers	HMEC	breast
5	chr5:178071400-178072600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:178071400-178072600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr5:178071600-178072400	Enhancers	NHDF-Ad	bronchial
8	chr5:178071600-178072400	Enhancers	NHEK	skin
9	chr5:178071600-178072600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:178071600-178072600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:178071600-178072600	Enhancers	HUVEC	blood vessel
12	chr5:178072000-178072400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:178072000-178072400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:178072000-178072400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:178072000-178072400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:178072000-178072400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:178072200-178072600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:178072200-178072600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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