Variant report

Variant	rs1835372
Chromosome Location	chr3:156519027-156519028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156487668..156490241-chr3:156516348..156519090,2	K562	blood:
2	chr3:156517343..156519280-chr3:156530527..156533564,3	MCF-7	breast:
3	chr3:156517394..156521071-chr3:156534029..156536553,4	MCF-7	breast:
4	chr3:156498174..156501165-chr3:156515710..156519959,5	K562	blood:
5	chr3:156517713..156521186-chr3:156527728..156530502,3	MCF-7	breast:
6	chr3:156517201..156520390-chr3:156522150..156525155,3	K562	blood:
7	chr3:156518854..156521208-chr3:156532361..156536474,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240875	Chromatin interaction
ENSG00000230457	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10936037	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10936038	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711674	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717133	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492804	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497539	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072896	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13086516	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13097325	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1430410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560415	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560416	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680305	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59717073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776157	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7641929	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818684	0.81[AMR][1000 genomes]
rs9820830	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9837271	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858861	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1835372	LINC00886	cis	Nerve Tibial	GTEx
rs1835372	LINC00886	cis	Esophagus Muscularis	GTEx
rs1835372	LINC00886	cis	lung	GTEx
rs1835372	LINC00886	cis	Artery Tibial	GTEx
rs1835372	LINC00886	cis	Thyroid	GTEx
rs1835372	LINC00886	cis	Artery Aorta	GTEx
rs1835372	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs1835372	LINC00886	cis	Stomach	GTEx
rs1835372	LINC00886	cis	Esophagus Mucosa	GTEx
rs1835372	LINC00886	cis	Muscle Skeletal	GTEx
rs1835372	LINC00886	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156502800-156528400	Weak transcription	Esophagus	oesophagus
2	chr3:156502800-156529000	Weak transcription	Liver	Liver
3	chr3:156511000-156519600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:156511200-156529000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:156511600-156519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:156514000-156519600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:156514400-156525400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:156514400-156525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:156517400-156529000	Weak transcription	A549	lung
11	chr3:156518000-156519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:156518000-156519600	Strong transcription	NHEK	skin
13	chr3:156518000-156524800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:156518000-156529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:156518600-156519800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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