Variant report

Variant	rs683393
Chromosome Location	chr5:15513258-15513259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10041362	0.82[AFR][1000 genomes]
rs10059008	1.00[EUR][1000 genomes]
rs10063263	1.00[EUR][1000 genomes]
rs10077393	1.00[EUR][1000 genomes]
rs11133817	1.00[EUR][1000 genomes]
rs13356380	1.00[EUR][1000 genomes]
rs1529487	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16903864	1.00[EUR][1000 genomes]
rs16903892	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs188592	1.00[EUR][1000 genomes]
rs2402164	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28713425	1.00[EUR][1000 genomes]
rs28716171	1.00[EUR][1000 genomes]
rs2896211	1.00[EUR][1000 genomes]
rs304557	1.00[EUR][1000 genomes]
rs304559	1.00[EUR][1000 genomes]
rs304560	1.00[EUR][1000 genomes]
rs304561	1.00[EUR][1000 genomes]
rs304562	1.00[EUR][1000 genomes]
rs4701626	1.00[EUR][1000 genomes]
rs4701628	1.00[EUR][1000 genomes]
rs4701629	1.00[EUR][1000 genomes]
rs4702074	1.00[EUR][1000 genomes]
rs4702075	1.00[EUR][1000 genomes]
rs4702077	1.00[EUR][1000 genomes]
rs512861	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs532005	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs572051	1.00[EUR][1000 genomes]
rs575014	1.00[EUR][1000 genomes]
rs57991493	1.00[EUR][1000 genomes]
rs598853	1.00[EUR][1000 genomes]
rs609984	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs623156	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs629654	1.00[GIH][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs633807	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs652985	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554885	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs685706	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751952	1.00[EUR][1000 genomes]
rs73751955	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709371	1.00[EUR][1000 genomes]
rs7717617	1.00[EUR][1000 genomes]
rs9312884	1.00[EUR][1000 genomes]
rs9312886	1.00[EUR][1000 genomes]
rs9968651	1.00[EUR][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	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

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15501800-15523800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:15502000-15515000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:15502000-15522200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:15502600-15522400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:15502600-15535400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:15502800-15513600	Weak transcription	Right Ventricle	heart
7	chr5:15502800-15514600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:15502800-15521400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:15503400-15521000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:15503800-15521000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:15504600-15521200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:15505800-15517400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:15507000-15513400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:15510400-15514600	Enhancers	Dnd41	blood
15	chr5:15511200-15513600	Weak transcription	Fetal Kidney	kidney
16	chr5:15511200-15514000	Weak transcription	Brain Substantia Nigra	brain
17	chr5:15511200-15514600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:15511200-15514800	Weak transcription	Aorta	Aorta
19	chr5:15511200-15514800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:15511200-15515800	Weak transcription	Lung	lung
21	chr5:15511200-15517400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:15511200-15522000	Weak transcription	Fetal Brain Male	brain
23	chr5:15511200-15527400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:15511400-15514000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:15511400-15521000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:15511600-15514800	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:15511600-15514800	Weak transcription	Left Ventricle	heart
28	chr5:15511600-15514800	Weak transcription	Ovary	ovary
29	chr5:15511600-15514800	Weak transcription	Right Atrium	heart
30	chr5:15511600-15516400	Weak transcription	NHLF	lung
31	chr5:15511600-15521200	Weak transcription	Fetal Lung	lung
32	chr5:15511600-15522400	Weak transcription	HSMMtube	muscle
33	chr5:15511800-15513600	Weak transcription	Adipose Nuclei	Adipose
34	chr5:15511800-15521400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:15511800-15521400	Weak transcription	Osteobl	bone
36	chr5:15512000-15514400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:15512000-15514800	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:15512000-15514800	Weak transcription	Fetal Stomach	stomach
39	chr5:15512000-15514800	Weak transcription	NHDF-Ad	bronchial
40	chr5:15512000-15518800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:15512000-15522000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr5:15512200-15514800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:15512200-15515200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:15512200-15521600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:15512200-15524600	Weak transcription	HSMM	muscle
46	chr5:15512200-15571200	Weak transcription	HUVEC	blood vessel
47	chr5:15512400-15515000	Weak transcription	Brain Anterior Caudate	brain
48	chr5:15512400-15521200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:15512400-15521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:15512600-15521000	Weak transcription	Colon Smooth Muscle	Colon

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