Variant report

Variant	rs56898852
Chromosome Location	chr12:42958363-42958364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10128834	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11181553	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11181555	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11181556	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181560	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309366	1.00[ASN][1000 genomes]
rs12312958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321305	1.00[ASN][1000 genomes]
rs12321729	1.00[ASN][1000 genomes]
rs17091361	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2103410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930021	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6582403	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582405	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7308904	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7955255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7965297	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1036522	chr12:42926075-42961887	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42939800-42971000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:42941200-42963400	Weak transcription	NHEK	skin
3	chr12:42944000-42959800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:42945800-42963800	Weak transcription	Fetal Intestine Small	intestine
5	chr12:42946800-42975200	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:42947000-42958400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:42951800-42958600	Weak transcription	Fetal Lung	lung
8	chr12:42953000-42963400	Weak transcription	Stomach Mucosa	stomach
9	chr12:42954600-42959000	Weak transcription	Left Ventricle	heart
10	chr12:42955000-42958600	Weak transcription	Adipose Nuclei	Adipose
11	chr12:42955000-42959000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:42955400-42958600	Weak transcription	Osteobl	bone
13	chr12:42955400-42958800	Weak transcription	HSMMtube	muscle
14	chr12:42955600-42958600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:42955800-42958800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:42955800-42963400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:42956000-42958600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:42956000-42958800	Weak transcription	Fetal Heart	heart
19	chr12:42956000-42959200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:42956400-42958600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:42956600-42958600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:42956600-42958600	Weak transcription	HSMM	muscle
23	chr12:42957000-42958600	Strong transcription	HUVEC	blood vessel
24	chr12:42957600-42960600	Strong transcription	HMEC	breast
25	chr12:42957800-42958400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:42958000-42959800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr12:42958000-42960400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:42958200-42958400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:42958200-42958400	Strong transcription	Fetal Stomach	stomach
30	chr12:42958200-42958800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:42958200-42959200	Enhancers	Placenta	Placenta
32	chr12:42958200-42959800	Enhancers	Lung	lung
33	chr12:42958200-42959800	Enhancers	NH-A	brain
34	chr12:42958200-42960400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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