Variant report

Variant	rs6581518
Chromosome Location	chr12:64408678-64408679
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64406060..64409789-chr12:64614427..64616806,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174206	Chromatin interaction
ENSG00000243024	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10784376	0.82[EUR][1000 genomes]
rs10784377	0.82[EUR][1000 genomes]
rs10878099	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175237	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11836824	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12367875	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17710730	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2335389	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35136111	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35266586	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3930087	0.80[EUR][1000 genomes]
rs6421210	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581520	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581521	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581522	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581523	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581524	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581526	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581527	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581528	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7295635	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297628	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7299597	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308431	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7312152	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312345	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7316077	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958660	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967578	0.82[EUR][1000 genomes]
rs7970430	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7971280	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7974633	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978183	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978207	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv747	chr12:64391572-64423998	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
3	nsv437756	chr12:64392500-64411870	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64380200-64433000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:64382800-64432800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:64383800-64425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:64385000-64408800	Weak transcription	Hela-S3	cervix
5	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
6	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
7	chr12:64389400-64419200	Weak transcription	Fetal Kidney	kidney
8	chr12:64389400-64419200	Weak transcription	Fetal Lung	lung
9	chr12:64389600-64417400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:64395400-64412400	Weak transcription	HMEC	breast
11	chr12:64396000-64415600	Weak transcription	Fetal Brain Female	brain
12	chr12:64396400-64414000	Weak transcription	Psoas Muscle	Psoas
13	chr12:64397200-64411200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:64398000-64425200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:64400400-64418400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:64401400-64416000	Weak transcription	Ovary	ovary
17	chr12:64402000-64413200	Weak transcription	NHEK	skin
18	chr12:64402000-64413400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:64402000-64415800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:64402200-64419200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:64404400-64410400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:64404400-64411000	Weak transcription	HSMM	muscle
23	chr12:64404400-64415200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:64404400-64417400	Weak transcription	HSMMtube	muscle
25	chr12:64404600-64415800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:64404600-64420800	Weak transcription	NHDF-Ad	bronchial
27	chr12:64404600-64421200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:64404600-64422400	Weak transcription	NH-A	brain
29	chr12:64404800-64409800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:64404800-64412600	Weak transcription	A549	lung
31	chr12:64404800-64415200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:64405000-64408800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:64405000-64417200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:64405000-64421000	Weak transcription	NHLF	lung
35	chr12:64407000-64420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:64407600-64409200	Enhancers	Osteobl	bone
37	chr12:64407800-64408800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:64407800-64409200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:64407800-64410800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:64408200-64422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:64408600-64409600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:64408600-64409600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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