Variant report

Variant	rs9524561
Chromosome Location	chr13:95269009-95269010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1341267	0.85[JPT][hapmap]
rs1572935	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2298055	0.80[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2298056	0.85[JPT][hapmap]
rs2298057	0.80[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35253817	0.88[AFR][1000 genomes]
rs3742107	0.80[YRI][hapmap]
rs3897473	0.80[ASN][1000 genomes]
rs3897474	0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4238308	0.82[ASN][1000 genomes]
rs4296139	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4771890	0.81[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6492721	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6492723	0.82[ASN][1000 genomes]
rs6492725	0.85[JPT][hapmap]
rs7326576	0.86[JPT][hapmap]
rs7981788	0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9301981	1.00[YRI][hapmap]
rs9301983	0.84[AFR][1000 genomes]
rs9516437	0.82[YRI][hapmap]
rs9516443	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9516445	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9516448	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9524554	0.83[AFR][1000 genomes]
rs9524555	0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9524556	0.81[ASN][1000 genomes]
rs9524557	0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9524559	0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9524560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524562	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524566	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9524568	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9556405	0.87[AFR][1000 genomes]
rs9561645	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9524561	GPR180	cis	Muscle Skeletal	GTEx
rs9524561	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95276600	Weak transcription	Small Intestine	intestine
2	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
3	chr13:95254800-95272000	Weak transcription	Lung	lung
4	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
8	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
9	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
10	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
11	chr13:95255200-95272200	Weak transcription	Colon Smooth Muscle	Colon
12	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
13	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
15	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
17	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
18	chr13:95255800-95278000	Weak transcription	Hela-S3	cervix
19	chr13:95255800-95284000	Weak transcription	K562	blood
20	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr13:95256600-95272000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr13:95259000-95275400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:95259600-95275400	Weak transcription	Primary B cells from cord blood	blood
24	chr13:95259600-95275400	Weak transcription	Brain Hippocampus Middle	brain
25	chr13:95259800-95275800	Weak transcription	Gastric	stomach
26	chr13:95259800-95276000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr13:95259800-95282000	Weak transcription	Brain Germinal Matrix	brain
28	chr13:95260000-95270400	Weak transcription	HMEC	breast
29	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:95261200-95272000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:95261800-95275400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr13:95262200-95278200	Weak transcription	Brain Substantia Nigra	brain
33	chr13:95262600-95271000	Weak transcription	Brain Anterior Caudate	brain
34	chr13:95263400-95271400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr13:95263600-95276200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr13:95264000-95275400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:95264000-95275400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr13:95264000-95284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr13:95264200-95275400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr13:95264200-95275400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:95264200-95275400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr13:95264200-95275400	Weak transcription	Ovary	ovary
43	chr13:95264200-95275400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr13:95264200-95280200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
46	chr13:95264400-95275400	Weak transcription	Placenta	Placenta
47	chr13:95264600-95271800	Weak transcription	Fetal Lung	lung
48	chr13:95264600-95272000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr13:95264600-95275200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:95264600-95275400	Weak transcription	Brain Cingulate Gyrus	brain

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