Variant report

Variant	rs55642517
Chromosome Location	chr12:64247093-64247094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64243148..64249002-chr12:64249405..64253780,7	MCF-7	breast:
2	chr12:64235116..64240404-chr12:64242494..64248805,7	MCF-7	breast:
3	chr12:64237577..64240346-chr12:64245227..64250030,4	MCF-7	breast:
4	chr12:64246806..64249435-chr12:64262805..64265409,2	K562	blood:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11175184	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175185	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175188	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175189	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175197	0.96[ASN][1000 genomes]
rs11833808	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11835034	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228199	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229790	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12579795	0.81[EUR][1000 genomes]
rs17099866	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2335884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35143986	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072758	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55655348	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55760535	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55907605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930806	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56028204	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56080061	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56264182	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58424013	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59063572	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60031756	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581509	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581510	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66856673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67401817	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67684483	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67830727	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67880496	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67892056	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67993208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68188132	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136130	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7294327	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301437	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302672	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7304340	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305893	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7307108	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308850	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310327	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310329	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310575	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311611	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73313479	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73315321	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315365	0.98[ASN][1000 genomes]
rs7953208	0.97[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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	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
7	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
8	esv1797043	chr12:64237504-64256568	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
9	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64240400-64247400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:64240800-64256000	Weak transcription	Small Intestine	intestine
3	chr12:64241000-64247400	Weak transcription	Ovary	ovary
4	chr12:64241000-64251800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:64241000-64255600	Weak transcription	Left Ventricle	heart
6	chr12:64241000-64256000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:64241000-64256000	Weak transcription	HSMM	muscle
8	chr12:64241000-64257200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:64241000-64261200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:64241000-64268800	Weak transcription	Lung	lung
11	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
12	chr12:64243000-64251200	Weak transcription	NHLF	lung
13	chr12:64243400-64247800	Enhancers	Fetal Brain Male	brain
14	chr12:64243400-64263000	Weak transcription	NHEK	skin
15	chr12:64243600-64256200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:64243800-64251400	Weak transcription	Osteobl	bone
17	chr12:64244000-64247200	Weak transcription	Fetal Kidney	kidney
18	chr12:64244000-64247400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:64244000-64247400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:64244000-64250200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:64244000-64250200	Weak transcription	NHDF-Ad	bronchial
22	chr12:64244000-64250400	Weak transcription	Hela-S3	cervix
23	chr12:64244000-64251600	Weak transcription	HMEC	breast
24	chr12:64244000-64256000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:64244000-64263600	Weak transcription	Fetal Lung	lung
26	chr12:64244200-64250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:64244200-64251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:64244200-64251600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:64244400-64247400	Weak transcription	Brain Substantia Nigra	brain
30	chr12:64244400-64247800	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:64244400-64251200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:64244400-64256000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:64244600-64251200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:64244800-64255800	Weak transcription	Brain Anterior Caudate	brain
35	chr12:64246000-64247200	Enhancers	A549	lung
36	chr12:64246000-64247400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:64246200-64247400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:64246200-64247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:64246200-64247400	Weak transcription	Fetal Intestine Small	intestine
40	chr12:64246200-64250800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:64246200-64254600	Weak transcription	Pancreas	Pancrea
42	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
43	chr12:64246400-64247400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:64246400-64248000	Enhancers	Fetal Intestine Large	intestine
45	chr12:64246400-64253400	Weak transcription	Brain Germinal Matrix	brain
46	chr12:64246400-64256000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:64246400-64256200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:64246600-64247400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:64246600-64247400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:64247000-64247600	Enhancers	HepG2	liver

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