Variant report

Variant	rs1552842
Chromosome Location	chr12:58012163-58012164
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	chr12:58009848..58012356-chr12:58118975..58121392,2	MCF-7	breast:
2	chr12:57913091..57915646-chr12:58010883..58013272,4	K562	blood:

Variant related genes	Relation type
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000257499	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1027315	0.94[ASN][1000 genomes]
rs1038914	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564374	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873919	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277324	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2307095	0.96[ASN][1000 genomes]
rs2640610	0.87[ASN][1000 genomes]
rs34271193	0.83[ASN][1000 genomes]
rs6581147	0.81[ASN][1000 genomes]
rs7134861	0.83[ASN][1000 genomes]
rs7304145	0.91[ASN][1000 genomes]
rs7966795	0.94[ASN][1000 genomes]
rs923828	0.85[EUR][1000 genomes];0.94[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	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1552842	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1552842	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs1552842	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58013200	Weak transcription	Gastric	stomach
2	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
3	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
4	chr12:58008000-58012800	Weak transcription	HepG2	liver
5	chr12:58010200-58013600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:58010400-58013600	Strong transcription	Stomach Smooth Muscle	stomach
7	chr12:58010400-58014000	Weak transcription	Brain Substantia Nigra	brain
8	chr12:58010400-58014400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:58010600-58012200	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:58010600-58013000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:58010600-58014000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:58010600-58014000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:58010600-58014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:58010800-58013000	Weak transcription	Osteobl	bone
15	chr12:58010800-58013200	Weak transcription	Esophagus	oesophagus
16	chr12:58010800-58013600	Weak transcription	Brain Anterior Caudate	brain
17	chr12:58011400-58014600	Weak transcription	Ovary	ovary
18	chr12:58011600-58013400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:58011600-58018000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:58011800-58013200	Weak transcription	Left Ventricle	heart
21	chr12:58011800-58013200	Weak transcription	Right Atrium	heart
22	chr12:58011800-58014200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:58011800-58015000	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:58011800-58018800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:58012000-58012200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:58012000-58012800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:58012000-58013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:58012000-58013200	Weak transcription	Spleen	Spleen
29	chr12:58012000-58015000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:58012000-58015000	Weak transcription	K562	blood
31	chr12:58012000-58019000	Weak transcription	Aorta	Aorta

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