Variant report

Variant	rs12437552
Chromosome Location	chr15:58995825-58995826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11071396	0.90[CHB][hapmap];0.90[AMR][1000 genomes]
rs11852241	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12438114	0.80[CHB][hapmap]
rs1365772	0.82[LWK][hapmap]
rs1427280	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17236243	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs2114573	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2414606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414607	0.92[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28391588	0.92[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3933541	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394845	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[ASN][1000 genomes]
rs447299	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4774309	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs655348	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs681711	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes]
rs694335	0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs7164844	0.83[TSI][hapmap]
rs7164954	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7168275	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7170538	0.89[TSI][hapmap]
rs7173286	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7176436	0.91[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.87[ASN][1000 genomes]
rs7179724	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182060	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7183504	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8023706	0.91[AMR][1000 genomes]
rs8027998	0.92[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8036097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9646204	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.85[AMR][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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-58996400	Weak transcription	NHLF	lung
2	chr15:58977200-58998200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:58977200-59004400	Weak transcription	Ovary	ovary
4	chr15:58977200-59007800	Weak transcription	HepG2	liver
5	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:58982600-59008000	Weak transcription	Fetal Brain Male	brain
8	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
9	chr15:58985200-59005000	Weak transcription	HSMMtube	muscle
10	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:58987400-59012000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:58987600-59005000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:58987600-59007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:58989000-58997200	ZNF genes & repeats	GM12878-XiMat	blood
15	chr15:58989400-58996000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:58990000-58996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:58990000-58996000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:58990000-58996200	Weak transcription	Right Atrium	heart
20	chr15:58990000-58997600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:58990000-58998400	Weak transcription	Gastric	stomach
22	chr15:58990000-58998400	Weak transcription	Right Ventricle	heart
23	chr15:58990000-58998800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:58990000-59004800	Weak transcription	Pancreas	Pancrea
25	chr15:58990000-59005000	Weak transcription	Spleen	Spleen
26	chr15:58990000-59005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:58990200-58996000	Weak transcription	Lung	lung
29	chr15:58991400-58996400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:58991600-58996800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:58991600-59005200	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:58991800-59005000	Weak transcription	Liver	Liver
33	chr15:58991800-59005000	Weak transcription	Fetal Kidney	kidney
34	chr15:58991800-59005000	Weak transcription	HMEC	breast
35	chr15:58991800-59012200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:58992000-58996000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:58992000-58996600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:58992000-59002600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:58992000-59005000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:58992000-59009000	Weak transcription	Placenta	Placenta
41	chr15:58992000-59010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:58992000-59015800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:58992000-59023000	Weak transcription	Esophagus	oesophagus
44	chr15:58992000-59023800	Weak transcription	Aorta	Aorta
45	chr15:58992200-59004400	Weak transcription	Fetal Muscle Leg	muscle
46	chr15:58992200-59008600	Weak transcription	Fetal Lung	lung
47	chr15:58992400-58996800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:58992400-58997600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:58992400-58998200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:58992400-59004600	Weak transcription	Fetal Muscle Trunk	muscle

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