Variant report

Variant	rs17100013
Chromosome Location	chr12:64419027-64419028
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	chr12:64412343..64415167-chr12:64418883..64421225,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12296441	1.00[EUR][1000 genomes]
rs12302441	1.00[EUR][1000 genomes]
rs12307017	1.00[EUR][1000 genomes]
rs12313251	1.00[EUR][1000 genomes]
rs12315032	1.00[EUR][1000 genomes]
rs12316287	1.00[EUR][1000 genomes]
rs12318085	1.00[EUR][1000 genomes]
rs12320688	1.00[EUR][1000 genomes]
rs17099997	0.94[YRI][hapmap];1.00[EUR][1000 genomes]
rs17100007	0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17100009	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55801058	1.00[EUR][1000 genomes]
rs57074356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57138272	1.00[EUR][1000 genomes]
rs57140731	1.00[EUR][1000 genomes]
rs57540857	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57937852	1.00[EUR][1000 genomes]
rs58129443	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59161915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60392489	1.00[EUR][1000 genomes]
rs74097504	1.00[EUR][1000 genomes]
rs74097515	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74097516	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74097517	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74097545	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74097547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74099369	1.00[EUR][1000 genomes]
rs74099375	1.00[EUR][1000 genomes]
rs74099376	1.00[EUR][1000 genomes]
rs74099377	1.00[EUR][1000 genomes]
rs74099378	1.00[EUR][1000 genomes]
rs74099379	1.00[EUR][1000 genomes]
rs74099380	1.00[EUR][1000 genomes]
rs74099381	1.00[EUR][1000 genomes]
rs74099382	1.00[EUR][1000 genomes]
rs74099383	1.00[EUR][1000 genomes]
rs74099384	1.00[EUR][1000 genomes]
rs74099385	1.00[EUR][1000 genomes]
rs74099392	1.00[EUR][1000 genomes]
rs74099393	1.00[EUR][1000 genomes]
rs74099395	1.00[EUR][1000 genomes]
rs74099398	1.00[EUR][1000 genomes]
rs74099400	1.00[EUR][1000 genomes]
rs7961633	1.00[EUR][1000 genomes]
rs7961964	1.00[EUR][1000 genomes]
rs7976142	1.00[EUR][1000 genomes]
rs7976369	1.00[EUR][1000 genomes]
rs7977480	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr12:64385000-64425600	Weak transcription	Left Ventricle	heart
5	chr12:64388800-64429800	Weak transcription	Pancreas	Pancrea
6	chr12:64389400-64419200	Weak transcription	Fetal Kidney	kidney
7	chr12:64389400-64419200	Weak transcription	Fetal Lung	lung
8	chr12:64398000-64425200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:64402200-64419200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:64404600-64420800	Weak transcription	NHDF-Ad	bronchial
11	chr12:64404600-64421200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:64404600-64422400	Weak transcription	NH-A	brain
13	chr12:64405000-64421000	Weak transcription	NHLF	lung
14	chr12:64407000-64420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:64408200-64422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:64408800-64421000	Weak transcription	Adipose Nuclei	Adipose
17	chr12:64409400-64422000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:64409400-64429600	Weak transcription	Hela-S3	cervix
19	chr12:64409600-64422400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:64410000-64428600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:64411000-64421000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:64411400-64422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:64411400-64425600	Weak transcription	Fetal Intestine Small	intestine
24	chr12:64412000-64423800	Weak transcription	Aorta	Aorta
25	chr12:64413800-64422400	Weak transcription	NHEK	skin
26	chr12:64415000-64432400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:64415200-64419600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:64415200-64420200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:64415400-64422600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:64415800-64426000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:64416000-64420800	Weak transcription	Brain Anterior Caudate	brain
32	chr12:64416400-64421000	Weak transcription	A549	lung
33	chr12:64416600-64422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:64416600-64425400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:64416600-64432400	Weak transcription	Fetal Brain Female	brain
36	chr12:64417400-64420800	Weak transcription	Osteobl	bone
37	chr12:64417600-64419400	Weak transcription	Fetal Muscle Leg	muscle
38	chr12:64417600-64419800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:64417800-64419400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:64417800-64422400	Weak transcription	HSMMtube	muscle
41	chr12:64418000-64422400	Weak transcription	HSMM	muscle
42	chr12:64418400-64419600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:64418400-64420800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:64418400-64422000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:64418600-64419800	Enhancers	Ovary	ovary
46	chr12:64418600-64425200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:64418600-64456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:64418800-64419200	Enhancers	HMEC	breast
49	chr12:64418800-64421000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:64419000-64419200	Enhancers	Brain Substantia Nigra	brain

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