Variant report

Variant	rs4907125
Chromosome Location	chr1:85508601-85508602
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	chr1:85508206..85510652-chr1:85512172..85515558,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055732	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10782534	0.82[EUR][1000 genomes]
rs10782536	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10873669	0.85[EUR][1000 genomes]
rs10873670	0.85[EUR][1000 genomes]
rs10873672	0.85[EUR][1000 genomes]
rs10873676	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10873677	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10873678	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873679	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873682	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161495	0.85[EUR][1000 genomes]
rs11161496	0.84[EUR][1000 genomes]
rs11161497	0.80[EUR][1000 genomes]
rs11161498	0.81[EUR][1000 genomes]
rs11161499	0.85[EUR][1000 genomes]
rs11161501	0.80[EUR][1000 genomes]
rs11161502	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11161503	0.81[EUR][1000 genomes]
rs11161504	0.81[EUR][1000 genomes]
rs11161505	0.81[EUR][1000 genomes]
rs11161513	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161514	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11485283	0.84[EUR][1000 genomes]
rs11485284	0.85[EUR][1000 genomes]
rs11799517	0.81[EUR][1000 genomes]
rs11804248	0.81[EUR][1000 genomes]
rs12022421	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12062414	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12091131	0.85[EUR][1000 genomes]
rs12130357	0.80[EUR][1000 genomes]
rs12138711	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12730688	0.85[EUR][1000 genomes]
rs1439130	0.83[EUR][1000 genomes]
rs1837328	0.81[EUR][1000 genomes]
rs2389792	0.81[EUR][1000 genomes]
rs2389793	0.81[EUR][1000 genomes]
rs2486755	0.85[EUR][1000 genomes]
rs3850430	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3861690	0.81[EUR][1000 genomes]
rs3895846	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs486751	0.85[EUR][1000 genomes]
rs488710	0.85[EUR][1000 genomes]
rs4907017	0.85[EUR][1000 genomes]
rs4907018	0.85[EUR][1000 genomes]
rs4907118	0.85[EUR][1000 genomes]
rs4907123	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs495786	0.84[EUR][1000 genomes]
rs499539	0.85[EUR][1000 genomes]
rs513430	0.85[EUR][1000 genomes]
rs515303	0.84[EUR][1000 genomes]
rs530486	0.85[EUR][1000 genomes]
rs531423	0.85[EUR][1000 genomes]
rs589653	0.85[EUR][1000 genomes]
rs600536	0.85[EUR][1000 genomes]
rs603746	0.85[EUR][1000 genomes]
rs625045	0.85[EUR][1000 genomes]
rs631267	0.85[EUR][1000 genomes]
rs632545	0.84[EUR][1000 genomes]
rs648660	0.85[EUR][1000 genomes]
rs650529	0.81[EUR][1000 genomes]
rs651916	0.85[EUR][1000 genomes]
rs6576736	0.85[EUR][1000 genomes]
rs662948	0.85[EUR][1000 genomes]
rs6677091	0.83[EUR][1000 genomes]
rs6685363	0.85[EUR][1000 genomes]
rs668860	0.85[EUR][1000 genomes]
rs6691674	0.85[EUR][1000 genomes]
rs6691970	0.85[EUR][1000 genomes]
rs6700622	0.85[EUR][1000 genomes]
rs6701779	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs677476	0.82[EUR][1000 genomes]
rs679167	0.85[EUR][1000 genomes]
rs726708	0.81[EUR][1000 genomes]
rs7516329	0.81[EUR][1000 genomes]
rs7516610	0.81[EUR][1000 genomes]
rs7516625	0.81[EUR][1000 genomes]
rs7522851	0.81[EUR][1000 genomes]
rs7541684	0.85[EUR][1000 genomes]
rs7549346	0.85[EUR][1000 genomes]
rs7553886	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4907125	MCOLN2	cis	Artery Tibial	GTEx
rs4907125	MCOLN3	cis	Thyroid	GTEx
rs4907125	MCOLN2	cis	Adipose Subcutaneous	GTEx
rs4907125	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs4907125	MCOLN2	cis	Thyroid	GTEx
rs4907125	MCOLN2	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85485400-85513000	Weak transcription	Pancreas	Pancrea
2	chr1:85486000-85513000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:85495000-85512800	Weak transcription	HMEC	breast
4	chr1:85496800-85512400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:85504600-85508800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:85505200-85511800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:85507800-85508800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:85507800-85510200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:85508400-85508800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:85508400-85513200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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