Variant report

Variant	rs680474
Chromosome Location	chr5:15515789-15515790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17647484	1.00[TSI][hapmap]
rs17647490	0.83[AMR][1000 genomes]
rs17704046	1.00[TSI][hapmap]
rs2964265	1.00[TSI][hapmap]
rs2964271	1.00[TSI][hapmap]
rs6867762	1.00[TSI][hapmap]
rs7736101	1.00[TSI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs680474	HP	trans	brain	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15501800-15523800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:15502000-15522200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:15502600-15522400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:15502600-15535400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:15502800-15521400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:15503400-15521000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:15503800-15521000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:15504600-15521200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:15505800-15517400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:15511200-15515800	Weak transcription	Lung	lung
11	chr5:15511200-15517400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:15511200-15522000	Weak transcription	Fetal Brain Male	brain
13	chr5:15511200-15527400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:15511400-15521000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:15511600-15516400	Weak transcription	NHLF	lung
16	chr5:15511600-15521200	Weak transcription	Fetal Lung	lung
17	chr5:15511600-15522400	Weak transcription	HSMMtube	muscle
18	chr5:15511800-15521400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:15511800-15521400	Weak transcription	Osteobl	bone
20	chr5:15512000-15518800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:15512000-15522000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:15512200-15521600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:15512200-15524600	Weak transcription	HSMM	muscle
24	chr5:15512200-15571200	Weak transcription	HUVEC	blood vessel
25	chr5:15512400-15521200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:15512400-15521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:15512600-15521000	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:15513000-15515800	Enhancers	Fetal Heart	heart
29	chr5:15513800-15517600	Weak transcription	Right Ventricle	heart
30	chr5:15514000-15515800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:15514600-15519000	Weak transcription	Dnd41	blood
32	chr5:15514800-15515800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr5:15514800-15515800	Enhancers	Right Atrium	heart
34	chr5:15515000-15515800	Enhancers	Brain Substantia Nigra	brain
35	chr5:15515200-15516200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:15515200-15521600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:15515200-15526600	Weak transcription	Ovary	ovary
38	chr5:15515200-15532800	Weak transcription	Aorta	Aorta
39	chr5:15515400-15517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:15515400-15521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:15515400-15521000	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:15515600-15516000	Genic enhancers	NHDF-Ad	bronchial
43	chr5:15515600-15516400	Weak transcription	Brain Angular Gyrus	brain
44	chr5:15515600-15516800	Weak transcription	Fetal Stomach	stomach
45	chr5:15515600-15518800	Weak transcription	Left Ventricle	heart
46	chr5:15515600-15521000	Weak transcription	Adipose Nuclei	Adipose
47	chr5:15515600-15521000	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:15515600-15521200	Weak transcription	Brain Anterior Caudate	brain
49	chr5:15515600-15525000	Weak transcription	Psoas Muscle	Psoas

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