Variant report

Variant	rs12968552
Chromosome Location	chr18:44702502-44702503
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
2	chr18:44675406..44678402-chr18:44700257..44702641,2	K562	blood:
3	chr18:44693298..44695901-chr18:44700902..44702609,2	K562	blood:
4	chr18:44675848..44678361-chr18:44699497..44704011,6	MCF-7	breast:
5	chr18:44495357..44497403-chr18:44700842..44702618,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078043	Chromatin interaction
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12953864	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13381713	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1434529	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512238	0.91[ASN][1000 genomes]
rs16954921	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16954999	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1836259	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289133	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2571002	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2571004	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571005	0.91[EUR][1000 genomes]
rs2571006	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571007	0.86[EUR][1000 genomes]
rs2571008	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2571010	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2571017	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2576052	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2576057	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2576058	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2635051	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2635052	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2635054	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2635056	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668758	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668759	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668761	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2668762	0.86[EUR][1000 genomes]
rs2668763	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2668784	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2684819	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2684833	0.91[EUR][1000 genomes]
rs2684851	0.82[EUR][1000 genomes]
rs28718304	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55730206	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7239323	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8085634	0.87[EUR][1000 genomes]
rs9953157	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9956809	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9961383	0.88[AFR][1000 genomes];0.89[EUR][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	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv3412252	chr18:44684003-44711534	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44700800-44703000	Active TSS	Colonic Mucosa	Colon
2	chr18:44701000-44702800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr18:44701000-44703000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:44701200-44702800	Active TSS	Fetal Muscle Trunk	muscle
5	chr18:44701200-44702800	Active TSS	Pancreas	Pancrea
6	chr18:44701200-44703000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr18:44701200-44703000	Active TSS	Aorta	Aorta
8	chr18:44701200-44703000	Active TSS	Psoas Muscle	Psoas
9	chr18:44701200-44703200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr18:44701400-44702800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr18:44701400-44703000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr18:44701400-44703000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr18:44701400-44703000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:44701400-44703000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:44701400-44703000	Active TSS	Ovary	ovary
16	chr18:44701400-44703000	Active TSS	Right Atrium	heart
17	chr18:44701400-44703000	Active TSS	NHDF-Ad	bronchial
18	chr18:44701400-44703000	Active TSS	NHLF	lung
19	chr18:44701600-44702800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr18:44701600-44702800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr18:44701600-44702800	Active TSS	Placenta	Placenta
22	chr18:44701600-44702800	Active TSS	Lung	lung
23	chr18:44701600-44702800	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr18:44701600-44702800	Active TSS	Stomach Mucosa	stomach
25	chr18:44701600-44702800	Active TSS	GM12878-XiMat	blood
26	chr18:44701600-44703000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr18:44701600-44703000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr18:44701600-44703000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr18:44701600-44703000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:44701600-44703000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:44701600-44703000	Active TSS	Fetal Intestine Large	intestine
32	chr18:44701600-44703000	Active TSS	Fetal Intestine Small	intestine
33	chr18:44701600-44703000	Active TSS	Fetal Kidney	kidney
34	chr18:44701600-44703000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr18:44701600-44703000	Active TSS	Fetal Thymus	thymus
36	chr18:44701600-44703000	Active TSS	Left Ventricle	heart
37	chr18:44701600-44703000	Active TSS	HSMM	muscle
38	chr18:44701600-44703000	Active TSS	HSMMtube	muscle
39	chr18:44701600-44703000	Active TSS	NH-A	brain
40	chr18:44701600-44703200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr18:44701600-44703200	Active TSS	Stomach Smooth Muscle	stomach
42	chr18:44701600-44703200	Active TSS	HepG2	liver
43	chr18:44701800-44702800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr18:44701800-44702800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:44701800-44702800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr18:44701800-44702800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr18:44701800-44702800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr18:44701800-44702800	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr18:44701800-44702800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr18:44701800-44702800	Active TSS	Esophagus	oesophagus

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