Variant report

Variant	rs10515676
Chromosome Location	chr5:152013887-152013888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10037655	0.81[AMR][1000 genomes]
rs10041396	0.81[AMR][1000 genomes]
rs10041415	0.81[AMR][1000 genomes]
rs10054152	0.80[AMR][1000 genomes]
rs10056328	0.81[AMR][1000 genomes]
rs10155517	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10515675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11167584	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11167585	0.82[AMR][1000 genomes]
rs11956651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188564	0.82[EUR][1000 genomes]
rs12515178	0.81[AMR][1000 genomes]
rs12518097	0.82[AMR][1000 genomes]
rs13359939	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13361438	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452991	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17453481	0.93[EUR][1000 genomes]
rs17453530	0.93[EUR][1000 genomes]
rs17453740	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17453775	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17454420	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17455800	0.85[EUR][1000 genomes]
rs17550343	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565365	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565470	0.85[EUR][1000 genomes]
rs17565505	0.83[EUR][1000 genomes]
rs17565693	0.90[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2961756	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2961760	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2961765	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2961766	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2964230	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2964231	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3923209	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4246033	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4391148	0.80[AMR][1000 genomes]
rs4398624	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4406125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478308	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4484412	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4557395	0.94[EUR][1000 genomes]
rs4580766	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4610448	0.83[AMR][1000 genomes]
rs4618416	0.80[AMR][1000 genomes]
rs4958316	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958317	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958320	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958321	0.81[AMR][1000 genomes]
rs4958322	0.81[AMR][1000 genomes]
rs4958323	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958324	0.80[AMR][1000 genomes]
rs4958560	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958561	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4958562	0.94[EUR][1000 genomes]
rs4958564	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4958566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958567	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4958568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958569	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958570	0.82[AMR][1000 genomes]
rs55648729	0.98[EUR][1000 genomes]
rs55786399	0.93[EUR][1000 genomes]
rs56014830	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67979431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6863717	0.80[AMR][1000 genomes]
rs6869129	0.80[AMR][1000 genomes]
rs6871699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876403	0.80[EUR][1000 genomes]
rs6876723	0.87[ASN][1000 genomes]
rs6884556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885111	0.80[AMR][1000 genomes]
rs6885419	0.80[AMR][1000 genomes]
rs6895969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795376	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72795379	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72795389	0.93[EUR][1000 genomes]
rs72797226	0.91[ASN][1000 genomes]
rs72797233	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797237	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797241	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797243	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72797251	0.97[EUR][1000 genomes]
rs72797254	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72797262	0.98[EUR][1000 genomes]
rs72797296	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72799113	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7730088	0.80[AMR][1000 genomes]
rs9324734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv5074	chr5:152010691-152055779	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10515676	IL17B	cis	cerebellum	SCAN
rs10515676	SLC26A2	cis	cerebellum	SCAN
rs10515676	IL17B	cis	parietal	SCAN
rs10515676	GLRA1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152002600-152014000	Weak transcription	Brain Substantia Nigra	brain
2	chr5:152004200-152014200	Weak transcription	Spleen	Spleen
3	chr5:152006400-152014400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:152008400-152022800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:152009000-152016800	Enhancers	Fetal Brain Female	brain
6	chr5:152011800-152021800	Weak transcription	Aorta	Aorta
7	chr5:152012200-152014600	Enhancers	Adipose Nuclei	Adipose
8	chr5:152012200-152014800	Enhancers	Fetal Brain Male	brain
9	chr5:152012600-152014000	Weak transcription	Fetal Kidney	kidney
10	chr5:152012800-152014200	Weak transcription	Right Atrium	heart
11	chr5:152012800-152014400	Weak transcription	Right Ventricle	heart
12	chr5:152012800-152018000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:152013400-152015000	Enhancers	Brain Hippocampus Middle	brain
14	chr5:152013400-152015200	Enhancers	Brain Germinal Matrix	brain
15	chr5:152013400-152015400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:152013600-152014400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:152013600-152014800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:152013600-152015000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:152013600-152015400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:152013600-152018400	Weak transcription	Fetal Lung	lung
21	chr5:152013800-152014600	Enhancers	Placenta Amnion	Placenta Amnion
22	chr5:152013800-152014800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:152013800-152014800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr5:152013800-152014800	Enhancers	Brain Anterior Caudate	brain
25	chr5:152013800-152015000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:152013800-152015000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr5:152013800-152015200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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