Variant report

Variant	rs3860174
Chromosome Location	chr9:116794619-116794620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1008138	0.91[CHB][hapmap]
rs10739398	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes]
rs10759669	0.82[CHB][hapmap]
rs10759675	0.87[EUR][1000 genomes]
rs10759676	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs10817545	0.82[CHB][hapmap]
rs10817546	0.82[CHB][hapmap]
rs10817547	0.81[CHB][hapmap]
rs10817548	0.81[CHB][hapmap]
rs10817552	0.88[EUR][1000 genomes]
rs10817555	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs10817556	0.91[EUR][1000 genomes]
rs10817558	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982026	0.84[EUR][1000 genomes]
rs10982029	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs10982031	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs10982032	0.89[EUR][1000 genomes]
rs10982034	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10982042	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11788633	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs11788661	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs11788667	0.87[EUR][1000 genomes]
rs11790678	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11791155	0.81[CHB][hapmap]
rs11791230	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs12551686	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12682865	0.81[CHB][hapmap]
rs12686226	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12686727	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs13298270	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs1330171	0.81[CHB][hapmap]
rs1408115	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs1590367	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965753	0.95[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2078305	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116407	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2418263	0.81[CHB][hapmap]
rs35841848	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748182	0.88[EUR][1000 genomes]
rs3748183	0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs4978561	0.88[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs4978562	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs4979310	0.82[CHB][hapmap]
rs4979311	0.81[CHB][hapmap]
rs4979316	0.81[CHB][hapmap]
rs4979317	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs4979318	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs4979319	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[EUR][1000 genomes]
rs4979320	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs4979321	0.91[CHB][hapmap]
rs4979322	0.91[CHB][hapmap];0.88[EUR][1000 genomes]
rs4979323	0.86[CHB][hapmap]
rs4979324	0.86[CHB][hapmap]
rs4979326	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs4979327	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4979331	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7020561	0.81[CHB][hapmap]
rs7023499	0.82[CHB][hapmap]
rs7026668	0.86[CHB][hapmap]
rs7030167	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs7032729	0.81[CHB][hapmap]
rs7035891	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7041360	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs7041487	0.86[CHB][hapmap]
rs7041524	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[EUR][1000 genomes]
rs7042021	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs7850217	0.81[CHB][hapmap]
rs7858120	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs942286	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs942287	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes]
rs9695257	0.82[CHB][hapmap]

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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3860174	COL27A1,MIR455	cis	substantia nigra	BrainEAC

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:116766000-116798000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:116766200-116799000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:116773600-116809200	Weak transcription	Fetal Heart	heart
7	chr9:116774200-116798400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:116780200-116798600	Weak transcription	Colonic Mucosa	Colon
9	chr9:116780600-116796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:116780800-116796800	Weak transcription	Brain Angular Gyrus	brain
11	chr9:116780800-116798000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:116780800-116800200	Weak transcription	Esophagus	oesophagus
13	chr9:116781000-116797600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:116784000-116798000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr9:116785200-116796000	Weak transcription	NHDF-Ad	bronchial
16	chr9:116785200-116811200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:116785400-116798200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:116785400-116799000	Weak transcription	Brain Substantia Nigra	brain
19	chr9:116785400-116810600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:116785800-116798000	Weak transcription	NH-A	brain
21	chr9:116785800-116798400	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:116786400-116796800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:116786400-116798800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:116786800-116794800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:116786800-116799000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:116787000-116796400	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:116787000-116799200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:116787000-116800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:116787000-116803000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:116787000-116812800	Weak transcription	Primary B cells from cord blood	blood
31	chr9:116787200-116799200	Strong transcription	Fetal Intestine Small	intestine
32	chr9:116787400-116798400	Weak transcription	Left Ventricle	heart
33	chr9:116787400-116798600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:116787400-116800200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:116788000-116802400	Strong transcription	Adipose Nuclei	Adipose
36	chr9:116788200-116797400	Strong transcription	HSMMtube	muscle
37	chr9:116788200-116798800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:116788200-116800000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:116788400-116799600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:116788600-116798400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr9:116788800-116796600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:116789600-116795000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:116789600-116800600	Strong transcription	NHLF	lung
44	chr9:116789600-116808600	Weak transcription	HMEC	breast
45	chr9:116790600-116801400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:116790600-116801600	Strong transcription	Spleen	Spleen
47	chr9:116790600-116802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:116790600-116802600	Strong transcription	Liver	Liver
49	chr9:116791400-116794800	Weak transcription	Gastric	stomach
50	chr9:116791400-116795800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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