Variant report

Variant	rs9524566
Chromosome Location	chr13:95276735-95276736
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1341267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1572935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298055	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2298057	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35253817	0.93[ASN][1000 genomes]
rs3897473	0.92[ASN][1000 genomes]
rs3897474	0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4238308	0.94[ASN][1000 genomes]
rs4296139	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4465476	0.98[ASN][1000 genomes]
rs4771890	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492720	0.91[ASN][1000 genomes]
rs6492721	0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6492723	0.94[ASN][1000 genomes]
rs6492725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7326576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7981788	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9516445	0.92[ASN][1000 genomes]
rs9516448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524555	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9524556	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9524557	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9524559	0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs9524560	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9524561	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9524562	0.95[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9524563	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9524568	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556405	0.89[ASN][1000 genomes]
rs9561643	0.85[ASN][1000 genomes]
rs9561645	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9524566	GPR180	cis	lung	GTEx
rs9524566	GPR180	cis	Muscle Skeletal	GTEx
rs9524566	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
2	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
4	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
6	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
8	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
9	chr13:95255800-95278000	Weak transcription	Hela-S3	cervix
10	chr13:95255800-95284000	Weak transcription	K562	blood
11	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:95259800-95282000	Weak transcription	Brain Germinal Matrix	brain
13	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:95262200-95278200	Weak transcription	Brain Substantia Nigra	brain
15	chr13:95264000-95284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr13:95264200-95280200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
18	chr13:95264600-95282400	Weak transcription	Pancreas	Pancrea
19	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
20	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
21	chr13:95264800-95284600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr13:95265400-95286800	Weak transcription	A549	lung
23	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:95267600-95277400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr13:95268600-95281000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr13:95268800-95279600	Weak transcription	HUVEC	blood vessel
27	chr13:95268800-95283800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr13:95270000-95283400	Strong transcription	Dnd41	blood
29	chr13:95270400-95276800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr13:95270400-95283400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:95270600-95278800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:95270800-95277600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr13:95270800-95283200	Strong transcription	Osteobl	bone
34	chr13:95271000-95277200	Strong transcription	NHDF-Ad	bronchial
35	chr13:95271000-95280600	Strong transcription	Liver	Liver
36	chr13:95271000-95281200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr13:95271000-95283000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr13:95271000-95283600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:95271400-95277600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:95271400-95282200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:95271600-95281800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:95272400-95282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:95272600-95283400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:95273600-95277600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr13:95273600-95278400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr13:95274000-95278800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr13:95274000-95284400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr13:95274600-95277800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:95274800-95276800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:95274800-95277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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