Variant report

Variant	rs1922576
Chromosome Location	chr12:83092584-83092585
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	chr12:83080196..83081829-chr12:83092014..83094612,2	MCF-7	breast:
2	chr12:83088398..83090839-chr12:83090924..83092850,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10862497	0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11115342	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11115348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11115353	0.88[EUR][1000 genomes]
rs11115355	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11609532	0.92[EUR][1000 genomes]
rs11610988	0.80[EUR][1000 genomes]
rs11613168	0.80[EUR][1000 genomes]
rs11614435	0.88[EUR][1000 genomes]
rs11615763	0.80[EUR][1000 genomes]
rs11615765	0.80[EUR][1000 genomes]
rs12305736	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12307168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12422405	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12426166	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12579483	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs13377925	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17009812	0.84[EUR][1000 genomes]
rs17009851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009854	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17009856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009882	0.82[EUR][1000 genomes]
rs17009885	0.82[EUR][1000 genomes]
rs17009891	0.80[EUR][1000 genomes]
rs17009893	0.80[EUR][1000 genomes]
rs17009899	0.80[EUR][1000 genomes]
rs1922579	0.91[EUR][1000 genomes]
rs4620789	0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4882428	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657485	0.92[EUR][1000 genomes]
rs56298822	0.95[EUR][1000 genomes]
rs56396658	0.92[EUR][1000 genomes]
rs61485473	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539683	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7134747	0.85[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134766	0.95[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135486	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72615654	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7294890	0.95[CHB][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7303469	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7313778	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73354481	0.84[EUR][1000 genomes]
rs74106267	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83082200-83102200	Weak transcription	Lung	lung
2	chr12:83082600-83094600	Weak transcription	Left Ventricle	heart
3	chr12:83082800-83095200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:83082800-83099400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:83082800-83102000	Weak transcription	NHDF-Ad	bronchial
6	chr12:83082800-83102200	Weak transcription	Pancreas	Pancrea
7	chr12:83083600-83101800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:83084000-83101400	Weak transcription	Fetal Kidney	kidney
9	chr12:83084600-83093400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:83084600-83101200	Weak transcription	Fetal Stomach	stomach
11	chr12:83084800-83092800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:83084800-83101400	Weak transcription	GM12878-XiMat	blood
13	chr12:83086000-83102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:83086200-83092800	Weak transcription	Fetal Brain Female	brain
15	chr12:83086200-83093200	Weak transcription	Fetal Brain Male	brain
16	chr12:83086400-83093200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:83086600-83122200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:83086800-83092800	Weak transcription	Brain Germinal Matrix	brain
19	chr12:83086800-83100800	Weak transcription	Fetal Heart	heart
20	chr12:83087200-83092600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:83087200-83105600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:83087400-83098800	Weak transcription	Fetal Lung	lung
23	chr12:83087400-83101200	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:83087400-83106400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:83089400-83095800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:83089600-83092600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:83089600-83092600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:83089600-83092800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:83089800-83092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:83090000-83092600	Weak transcription	Brain Anterior Caudate	brain
31	chr12:83090200-83092800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:83090600-83092600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:83091200-83092800	Enhancers	Brain Substantia Nigra	brain
34	chr12:83091400-83094000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:83091600-83092600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:83091600-83093000	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:83091600-83093400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:83092000-83092600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:83092000-83092800	Enhancers	Brain Hippocampus Middle	brain
40	chr12:83092000-83092800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:83092000-83093400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:83092000-83093600	Enhancers	Colon Smooth Muscle	Colon
43	chr12:83092200-83093000	Enhancers	HMEC	breast
44	chr12:83092400-83092800	Enhancers	Brain Angular Gyrus	brain

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