Variant report

Variant	rs6539683
Chromosome Location	chr12:83124031-83124032
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	chr12:83122848..83125813-chr12:83126574..83128906,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10506878	0.89[EUR][1000 genomes]
rs10862497	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11115342	0.81[EUR][1000 genomes]
rs11115348	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11115355	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610988	0.87[EUR][1000 genomes]
rs11611431	0.89[EUR][1000 genomes]
rs11613168	0.87[EUR][1000 genomes]
rs11615763	0.87[EUR][1000 genomes]
rs11615765	0.87[EUR][1000 genomes]
rs12305736	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12307168	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12422405	0.86[ASN][1000 genomes]
rs12423043	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426166	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13377925	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17009851	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17009856	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17009882	0.85[EUR][1000 genomes]
rs17009885	0.85[EUR][1000 genomes]
rs17009891	0.87[EUR][1000 genomes]
rs17009893	0.87[EUR][1000 genomes]
rs17009899	0.87[EUR][1000 genomes]
rs1922576	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4620789	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4882428	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61485473	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7134747	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7134766	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135486	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72615654	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294890	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303469	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313778	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74106267	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7961953	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975647	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
4	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
5	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
6	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
7	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
8	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv2755991	chr12:83105631-83248605	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv469491	chr12:83108395-83203742	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv559543	chr12:83108395-83203742	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83102400-83138800	Weak transcription	Fetal Kidney	kidney
2	chr12:83102600-83140600	Weak transcription	Pancreas	Pancrea
3	chr12:83102800-83134000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:83106800-83133800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:83107000-83127800	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:83112600-83124200	Weak transcription	Fetal Lung	lung
7	chr12:83113000-83138600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:83113200-83124600	Weak transcription	Fetal Brain Male	brain
9	chr12:83115200-83138200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:83115400-83138800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:83115800-83138000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:83118800-83124800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:83119800-83134200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:83120200-83133000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:83121000-83126600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:83121200-83124200	Strong transcription	Fetal Stomach	stomach
17	chr12:83121400-83124400	Weak transcription	Colonic Mucosa	Colon
18	chr12:83121400-83128000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:83122000-83138600	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:83122000-83149000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:83122200-83125200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:83122800-83124400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:83122800-83125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:83122800-83125000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:83122800-83140200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:83122800-83143600	Weak transcription	Lung	lung
27	chr12:83123000-83134600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:83123000-83138000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:83123000-83140400	Weak transcription	Gastric	stomach
30	chr12:83123000-83140600	Weak transcription	Esophagus	oesophagus
31	chr12:83123600-83124200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:83123600-83124400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:83123600-83126400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:83123800-83128000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:83124000-83134400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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