Variant report

Variant	rs7038920
Chromosome Location	chr9:15724354-15724355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10119980	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10121391	0.90[EUR][1000 genomes]
rs10217374	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1039812	0.97[EUR][1000 genomes]
rs1039815	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1039816	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10732334	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10733296	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738407	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10756706	0.90[EUR][1000 genomes]
rs10810445	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10810447	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12350267	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1355172	0.97[EUR][1000 genomes]
rs1417974	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1417975	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1509311	0.91[EUR][1000 genomes]
rs1553727	0.91[EUR][1000 genomes]
rs1848583	0.91[EUR][1000 genomes]
rs1891208	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1935225	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1964706	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1970496	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs202321	0.90[EUR][1000 genomes]
rs2055773	0.97[EUR][1000 genomes]
rs2055774	0.97[EUR][1000 genomes]
rs2089618	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2136354	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2136357	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2175083	0.97[EUR][1000 genomes]
rs2185664	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2221706	0.87[EUR][1000 genomes]
rs2382531	0.90[EUR][1000 genomes]
rs2382533	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2382535	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2382536	0.91[EUR][1000 genomes]
rs276440	0.90[EUR][1000 genomes]
rs276442	0.90[EUR][1000 genomes]
rs3122701	0.84[EUR][1000 genomes]
rs398117	0.91[EUR][1000 genomes]
rs398178	0.90[EUR][1000 genomes]
rs401393	0.90[EUR][1000 genomes]
rs4146292	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4237140	0.91[EUR][1000 genomes]
rs4445326	0.91[EUR][1000 genomes]
rs4740623	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4741532	0.90[EUR][1000 genomes]
rs4741533	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4741536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4741537	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4741540	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6474941	0.91[EUR][1000 genomes]
rs6474947	0.90[EUR][1000 genomes]
rs6474949	0.97[EUR][1000 genomes]
rs6474956	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6474957	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6474961	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6474973	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7025247	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7035422	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7037893	0.85[EUR][1000 genomes]
rs7847148	0.94[EUR][1000 genomes]
rs7849159	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7859685	0.86[EUR][1000 genomes]
rs7865193	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7865391	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7866413	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7870315	0.91[EUR][1000 genomes]
rs7874094	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9298734	0.90[EUR][1000 genomes]
rs958870	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9919009	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2752286	chr9:15578017-15794897	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv892632	chr9:15590116-15869845	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv892633	chr9:15604746-15889411	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv466262	chr9:15615321-15727518	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv613657	chr9:15615321-15727518	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv613658	chr9:15636260-15727518	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv466263	chr9:15641279-15726057	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv613659	chr9:15641279-15726057	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv892634	chr9:15696501-15746168	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv32957	chr9:15720059-15737099	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7038920	CCDC171	cis	Esophagus Mucosa	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15676600-15725000	Weak transcription	Pancreas	Pancrea
2	chr9:15679800-15746800	Weak transcription	Ovary	ovary
3	chr9:15687600-15746600	Weak transcription	Aorta	Aorta
4	chr9:15699600-15728200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:15715200-15746200	Weak transcription	Left Ventricle	heart
6	chr9:15715600-15733800	Weak transcription	Brain Anterior Caudate	brain
7	chr9:15716000-15727800	Weak transcription	Fetal Thymus	thymus
8	chr9:15717400-15727600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:15718000-15749600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:15718400-15724800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:15718600-15746600	Weak transcription	Thymus	Thymus
12	chr9:15718800-15727800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:15720400-15733400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:15720600-15735200	Weak transcription	Adipose Nuclei	Adipose
15	chr9:15721600-15725000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:15722200-15726400	Enhancers	Fetal Lung	lung
17	chr9:15722600-15725400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:15722800-15725200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:15722800-15725400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr9:15723200-15724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr9:15723400-15724600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:15723400-15724600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:15723400-15725000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:15723400-15725000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:15723400-15726000	Weak transcription	Fetal Stomach	stomach
26	chr9:15723400-15728000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:15723400-15728800	Weak transcription	Fetal Brain Male	brain
28	chr9:15724000-15725000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:15724000-15725000	Enhancers	NHDF-Ad	bronchial
30	chr9:15724000-15725200	Enhancers	Osteobl	bone
31	chr9:15724200-15724600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:15724200-15725200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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