Variant report

Variant	rs10817286
Chromosome Location	chr9:100001077-100001078
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10122063	0.86[CEU][hapmap]
rs10125198	0.86[CEU][hapmap]
rs10125824	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10435868	0.85[CEU][hapmap]
rs10448274	0.86[CEU][hapmap]
rs10759521	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10759526	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759527	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817273	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10981278	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10981297	0.91[JPT][hapmap]
rs10981890	0.82[CEU][hapmap]
rs10981919	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs10981931	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs12685723	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1542506	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs1947717	0.82[CEU][hapmap]
rs2169456	0.86[CEU][hapmap]
rs2242187	0.89[CEU][hapmap]
rs2306097	0.89[CEU][hapmap]
rs3747489	0.86[CEU][hapmap]
rs3747493	0.89[CEU][hapmap]
rs3747496	0.89[CEU][hapmap]
rs4237189	0.86[CEU][hapmap]
rs4313271	0.89[CEU][hapmap]
rs4366181	0.89[CEU][hapmap]
rs4523385	0.85[CEU][hapmap]
rs4742689	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs4743076	0.85[CEU][hapmap]
rs4743077	0.89[CEU][hapmap]
rs4743084	0.86[CEU][hapmap]
rs4743087	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs4743088	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs6478025	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6478095	0.89[CEU][hapmap]
rs7858579	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10817286	CCDC180	cis	Artery Tibial	GTEx
rs10817286	RP11-520B13.4	cis	Thyroid	GTEx
rs10817286	ANKRD18CP	cis	Thyroid	GTEx
rs10817286	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs10817286	RP11-498P14.5	cis	Thyroid	GTEx
rs10817286	RP11-498P14.5	cis	lung	GTEx
rs10817286	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99998400-100001800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:99998600-100002200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr9:99999000-100001800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr9:99999000-100002000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:99999000-100002000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr9:99999200-100001800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr9:99999200-100001800	Active TSS	K562	blood
8	chr9:99999200-100002000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr9:99999400-100001400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr9:99999400-100001800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:99999400-100001800	Active TSS	HMEC	breast
12	chr9:99999400-100002000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr9:99999600-100001200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:99999600-100001200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:99999600-100001200	Active TSS	Osteobl	bone
16	chr9:99999600-100001400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:99999600-100001400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:99999600-100001400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:99999600-100001400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:99999600-100001400	Active TSS	Brain Angular Gyrus	brain
21	chr9:99999600-100001400	Active TSS	Brain Anterior Caudate	brain
22	chr9:99999600-100001600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr9:99999600-100001600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:99999600-100001600	Active TSS	Brain Hippocampus Middle	brain
25	chr9:99999600-100001600	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr9:99999600-100001600	Active TSS	Fetal Intestine Large	intestine
27	chr9:99999600-100001600	Active TSS	HepG2	liver
28	chr9:99999600-100001800	Active TSS	Brain Cingulate Gyrus	brain
29	chr9:99999800-100001200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:99999800-100001200	Active TSS	Fetal Intestine Small	intestine
31	chr9:99999800-100001200	Active TSS	Rectal Smooth Muscle	rectum
32	chr9:99999800-100001200	Active TSS	HSMM	muscle
33	chr9:99999800-100001400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:99999800-100001400	Active TSS	Colonic Mucosa	Colon
35	chr9:99999800-100001600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:99999800-100001600	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr9:99999800-100001600	Active TSS	Ovary	ovary
38	chr9:99999800-100001600	Active TSS	Right Ventricle	heart
39	chr9:99999800-100001600	Active TSS	Stomach Smooth Muscle	stomach
40	chr9:99999800-100001600	Active TSS	Thymus	Thymus
41	chr9:99999800-100001600	Active TSS	Hela-S3	cervix
42	chr9:99999800-100001600	Active TSS	NHEK	skin
43	chr9:99999800-100001800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:99999800-100002000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:99999800-100002000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr9:100000000-100001200	Active TSS	Fetal Stomach	stomach
47	chr9:100000000-100001200	Active TSS	Pancreas	Pancrea
48	chr9:100000000-100001200	Active TSS	Dnd41	blood
49	chr9:100000000-100001400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:100000000-100001400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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