Variant report

Variant	rs12439189
Chromosome Location	chr15:58902769-58902770
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10851639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071396	0.81[CHB][hapmap]
rs12438114	0.84[CHB][hapmap]
rs12438487	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12591291	0.83[ASN][1000 genomes]
rs12591543	0.80[ASN][1000 genomes]
rs12592750	0.81[ASN][1000 genomes]
rs12905173	0.82[ASN][1000 genomes]
rs12906705	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs12908449	0.82[ASN][1000 genomes]
rs1365772	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16940587	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs16940589	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs16940651	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1820548	0.83[ASN][1000 genomes]
rs1869133	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1869135	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2081703	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2303532	0.80[ASN][1000 genomes]
rs2305421	0.81[ASN][1000 genomes]
rs28417700	0.82[ASN][1000 genomes]
rs28457680	0.82[ASN][1000 genomes]
rs28573205	0.81[ASN][1000 genomes]
rs28584993	0.82[ASN][1000 genomes]
rs28600144	0.83[ASN][1000 genomes]
rs28678478	0.82[ASN][1000 genomes]
rs3764196	1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs394845	0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap]
rs4774309	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs4775084	0.99[ASN][1000 genomes]
rs6494031	0.80[ASN][1000 genomes]
rs694335	0.95[MKK][hapmap]
rs7162952	0.91[ASN][1000 genomes]
rs7163733	0.83[JPT][hapmap]
rs7164620	0.83[ASN][1000 genomes]
rs7165035	0.83[ASN][1000 genomes]
rs7165259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7166076	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7166325	0.83[JPT][hapmap]
rs7174414	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7180550	0.83[ASN][1000 genomes]
rs7182060	0.81[LWK][hapmap];0.94[YRI][hapmap]
rs8033565	0.82[ASN][1000 genomes]
rs8036005	0.83[ASN][1000 genomes]
rs8039791	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9920042	0.83[ASN][1000 genomes]
rs9920720	0.83[JPT][hapmap]
rs9921024	0.82[JPT][hapmap];0.83[ASN][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	nsv1551	chr15:58891639-58936580	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:58882600-58904000	Weak transcription	Gastric	stomach
5	chr15:58882600-58907600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:58883200-58904600	Strong transcription	HSMM	muscle
7	chr15:58885800-58906800	Weak transcription	Fetal Brain Male	brain
8	chr15:58887200-58906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:58887800-58905200	Weak transcription	Brain Germinal Matrix	brain
10	chr15:58888000-58906200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:58888400-58920000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:58889600-58904600	Weak transcription	Colonic Mucosa	Colon
13	chr15:58889600-58905200	Weak transcription	Fetal Brain Female	brain
14	chr15:58889600-58919800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:58889800-58918800	Weak transcription	Osteobl	bone
16	chr15:58889800-58921000	Weak transcription	Ovary	ovary
17	chr15:58890000-58904400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:58890000-58906200	Weak transcription	Small Intestine	intestine
19	chr15:58890800-58905200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:58891000-58906800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:58893800-58906200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:58893800-58906200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:58894400-58905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:58894800-58904400	Weak transcription	Fetal Stomach	stomach
26	chr15:58894800-58904400	Weak transcription	Spleen	Spleen
27	chr15:58894800-58904600	Weak transcription	Aorta	Aorta
28	chr15:58894800-58906200	Strong transcription	Primary B cells from cord blood	blood
29	chr15:58894800-58906800	Weak transcription	Psoas Muscle	Psoas
30	chr15:58896600-58905000	Weak transcription	Lung	lung
31	chr15:58897200-58904000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:58897200-58904600	Weak transcription	Pancreas	Pancrea
33	chr15:58897400-58904200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:58897400-58905200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:58897600-58905000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:58898400-58904600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:58898600-58903800	Weak transcription	Fetal Intestine Large	intestine
38	chr15:58898600-58904400	Weak transcription	Fetal Intestine Small	intestine
39	chr15:58899200-58905000	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:58899200-58920200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr15:58899600-58906200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr15:58900000-58903000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:58900000-58904600	Strong transcription	Liver	Liver
44	chr15:58900000-58906000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:58900200-58902800	Enhancers	NHLF	lung
46	chr15:58900200-58904800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:58900200-58905000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:58900200-58908400	Weak transcription	Hela-S3	cervix
49	chr15:58900400-58903200	Strong transcription	Fetal Lung	lung
50	chr15:58900400-58903200	Strong transcription	Rectal Mucosa Donor 29	rectum

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