Variant report

Variant	rs13377925
Chromosome Location	chr12:83100716-83100717
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	chr12:83078166..83081005-chr12:83099084..83103387,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10506878	0.81[EUR][1000 genomes]
rs10862497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11115342	0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11115348	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11115353	0.91[EUR][1000 genomes]
rs11115355	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11609532	0.87[EUR][1000 genomes]
rs11610988	0.83[EUR][1000 genomes]
rs11611431	0.81[EUR][1000 genomes]
rs11613168	0.83[EUR][1000 genomes]
rs11614435	0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs11615763	0.83[EUR][1000 genomes]
rs11615765	0.83[EUR][1000 genomes]
rs12305736	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12307168	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12422405	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12423043	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12426166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12579483	0.82[CHB][hapmap]
rs17009851	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17009854	0.90[EUR][1000 genomes]
rs17009856	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009882	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs17009885	0.85[EUR][1000 genomes]
rs17009891	0.83[EUR][1000 genomes]
rs17009893	0.83[EUR][1000 genomes]
rs17009899	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1922576	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1922579	0.88[EUR][1000 genomes]
rs4620789	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4882428	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55657485	0.87[EUR][1000 genomes]
rs56298822	0.90[EUR][1000 genomes]
rs56396658	0.87[EUR][1000 genomes]
rs61485473	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6539683	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134747	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7134766	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135486	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72615654	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303469	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313778	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74106267	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961953	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7975647	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13377925	CYP26C1	trans	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83082200-83102200	Weak transcription	Lung	lung
2	chr12:83082800-83102000	Weak transcription	NHDF-Ad	bronchial
3	chr12:83082800-83102200	Weak transcription	Pancreas	Pancrea
4	chr12:83083600-83101800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:83084000-83101400	Weak transcription	Fetal Kidney	kidney
6	chr12:83084600-83101200	Weak transcription	Fetal Stomach	stomach
7	chr12:83084800-83101400	Weak transcription	GM12878-XiMat	blood
8	chr12:83086000-83102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:83086600-83122200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:83086800-83100800	Weak transcription	Fetal Heart	heart
11	chr12:83087200-83105600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:83087400-83101200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:83087400-83106400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:83092800-83102200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:83093000-83101000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:83093200-83122400	Weak transcription	Gastric	stomach
17	chr12:83093400-83101200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:83093600-83101000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:83093800-83100800	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:83094600-83101000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:83095400-83106600	Weak transcription	Fetal Intestine Large	intestine
22	chr12:83096000-83102000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:83096000-83105800	Weak transcription	Fetal Intestine Small	intestine
24	chr12:83096200-83100800	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:83096200-83101200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:83098000-83121200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:83098800-83106800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:83099000-83101600	Weak transcription	Fetal Lung	lung
29	chr12:83099200-83122400	Weak transcription	Esophagus	oesophagus
30	chr12:83099400-83102200	Enhancers	Brain Substantia Nigra	brain
31	chr12:83099400-83103800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:83099600-83101200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:83099600-83101200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:83100400-83102200	Enhancers	Brain Anterior Caudate	brain
35	chr12:83100400-83103200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:83100600-83102000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:83100600-83102200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:83100600-83102400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:83100600-83102800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:83100600-83103000	Enhancers	HUES48 Cell Line	embryonic stem cell

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