Variant report

Variant	rs12189348
Chromosome Location	chr5:15598350-15598351
allele	C/T
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:43)

rs_ID	r²[population]
rs1025328	0.88[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1025329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454921	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10520817	0.83[CEU][hapmap]
rs10520818	0.83[CEU][hapmap]
rs11953541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12187510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12189306	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12189375	0.81[CEU][hapmap]
rs12652710	0.87[ASN][1000 genomes]
rs12652729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12655307	0.91[CEU][hapmap]
rs12656824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12656926	0.87[ASN][1000 genomes]
rs12659622	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13170478	0.90[CHB][hapmap]
rs1429032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1549696	1.00[CEU][hapmap]
rs1582998	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16903918	0.91[CEU][hapmap]
rs17523312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17523716	0.91[CEU][hapmap]
rs17523908	0.91[CEU][hapmap]
rs17523929	0.90[CEU][hapmap]
rs17524082	0.87[CEU][hapmap]
rs17601883	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs17602097	0.91[CEU][hapmap]
rs17602228	0.91[CEU][hapmap]
rs17602477	0.81[CEU][hapmap]
rs17703976	0.91[CEU][hapmap]
rs2914762	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4509020	0.91[CEU][hapmap]
rs4510585	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4510586	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4702087	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs60120968	0.96[ASN][1000 genomes]
rs6877517	0.81[CEU][hapmap]
rs6879143	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs6892081	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7720476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7733676	0.91[CEU][hapmap]
rs891195	1.00[CEU][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv4732	chr5:15598325-15636520	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15578200-15600200	Weak transcription	Left Ventricle	heart
2	chr5:15581000-15604400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:15581600-15603400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:15584000-15599200	Weak transcription	HSMMtube	muscle
5	chr5:15585000-15604000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:15585000-15606400	Weak transcription	Adipose Nuclei	Adipose
7	chr5:15585000-15630200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:15585200-15600000	Weak transcription	HSMM	muscle
9	chr5:15585200-15601000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:15585200-15602000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:15585200-15605200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:15586000-15619800	Weak transcription	NHLF	lung
13	chr5:15586400-15598800	Weak transcription	Aorta	Aorta
14	chr5:15587400-15600200	Weak transcription	Lung	lung
15	chr5:15587800-15601000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:15587800-15601000	Weak transcription	Brain Anterior Caudate	brain
17	chr5:15588200-15598800	Weak transcription	Brain Substantia Nigra	brain
18	chr5:15588200-15605400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:15588400-15600400	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:15588400-15612600	Weak transcription	NHDF-Ad	bronchial
21	chr5:15588800-15603600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:15590800-15605000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:15593400-15606000	Weak transcription	HUVEC	blood vessel
24	chr5:15593400-15633400	Weak transcription	Fetal Lung	lung
25	chr5:15593600-15600000	Weak transcription	Fetal Stomach	stomach
26	chr5:15593600-15606200	Weak transcription	Fetal Brain Male	brain
27	chr5:15593600-15606400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:15593800-15601000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:15594800-15605000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:15595000-15601400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:15595200-15600200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:15595200-15607800	Weak transcription	Fetal Kidney	kidney
33	chr5:15595400-15600000	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:15595800-15600800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:15595800-15601000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:15596200-15601600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:15597400-15600600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:15597400-15600800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:15597400-15600800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:15597400-15604800	Weak transcription	Ovary	ovary
41	chr5:15597400-15605000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:15597800-15600000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:15598000-15600200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:15598000-15601000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:15598000-15601400	Enhancers	Fetal Heart	heart
46	chr5:15598200-15598400	Enhancers	Colon Smooth Muscle	Colon

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