Variant report

Variant	rs1638526
Chromosome Location	chr17:19848450-19848451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11204422	0.89[JPT][hapmap]
rs11867585	0.81[JPT][hapmap]
rs11870381	0.90[JPT][hapmap]
rs12449662	0.83[AMR][1000 genomes]
rs12450857	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12451841	0.90[JPT][hapmap]
rs12453720	0.86[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12942179	0.81[JPT][hapmap]
rs12943369	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12947713	0.90[JPT][hapmap]
rs1638525	0.85[AFR][1000 genomes]
rs1638527	0.95[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1638528	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs169413	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17604987	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17605101	0.86[EUR][1000 genomes]
rs17686798	0.90[JPT][hapmap]
rs17759959	0.90[JPT][hapmap]
rs203449	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203454	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203460	0.83[YRI][hapmap]
rs203462	0.83[YRI][hapmap]
rs203464	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs203467	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs203474	0.97[EUR][1000 genomes]
rs203475	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs203476	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203478	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs203479	0.83[YRI][hapmap]
rs203480	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2072337	1.00[JPT][hapmap]
rs2108981	0.86[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs28424266	0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34182788	0.81[EUR][1000 genomes]
rs34726000	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35925051	0.86[EUR][1000 genomes]
rs35979784	0.81[EUR][1000 genomes]
rs36097967	0.86[EUR][1000 genomes]
rs403021	0.93[EUR][1000 genomes]
rs4141185	1.00[JPT][hapmap]
rs427033	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4924808	0.90[JPT][hapmap]
rs4925054	0.86[CEU][hapmap]
rs4925075	0.90[JPT][hapmap]
rs4925082	0.90[JPT][hapmap]
rs56005410	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62066345	0.83[AMR][1000 genomes]
rs62066346	0.82[AMR][1000 genomes]
rs62066347	0.82[AMR][1000 genomes]
rs6587207	0.90[JPT][hapmap]
rs6813	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7207459	0.90[JPT][hapmap]
rs7209653	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215803	0.90[JPT][hapmap]
rs7222403	0.83[YRI][hapmap]
rs7224875	0.90[JPT][hapmap]
rs8065122	0.82[ASN][1000 genomes]
rs8068484	0.90[JPT][hapmap]
rs8075343	0.90[JPT][hapmap]
rs8079923	0.95[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8080190	0.90[JPT][hapmap]
rs850622	0.95[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs888424	0.90[JPT][hapmap]
rs9891503	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9893296	0.86[ASN][1000 genomes]
rs9897653	0.81[JPT][hapmap]
rs9901294	0.91[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915039	0.90[JPT][hapmap]
rs9944451	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1638526	AKAP10	cis	Lymphoblastoid	GTEx
rs1638526	AKAP10	cis	lymphoblastoid	seeQTL
rs1638526	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs1638526	AKAP10	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
3	chr17:19804000-19853000	Strong transcription	Dnd41	blood
4	chr17:19825200-19851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:19827600-19851600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:19827600-19852800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:19830600-19851200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:19831600-19851400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:19838600-19851600	Weak transcription	Psoas Muscle	Psoas
10	chr17:19839800-19849800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:19840000-19849400	Weak transcription	Colonic Mucosa	Colon
12	chr17:19840000-19851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:19840000-19879200	Weak transcription	Fetal Brain Male	brain
14	chr17:19841600-19848600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:19841600-19852800	Strong transcription	Primary B cells from cord blood	blood
16	chr17:19841800-19851600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr17:19841800-19852600	Strong transcription	Fetal Intestine Large	intestine
18	chr17:19842000-19850000	Weak transcription	Gastric	stomach
19	chr17:19842000-19850000	Weak transcription	Pancreas	Pancrea
20	chr17:19842000-19852600	Strong transcription	Hela-S3	cervix
21	chr17:19842400-19850000	Weak transcription	Aorta	Aorta
22	chr17:19842400-19851800	Strong transcription	Primary hematopoietic stem cells	blood
23	chr17:19842600-19851600	Strong transcription	GM12878-XiMat	blood
24	chr17:19843000-19850000	Weak transcription	Right Ventricle	heart
25	chr17:19843200-19848600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:19843200-19848800	Weak transcription	Esophagus	oesophagus
27	chr17:19843200-19848800	Weak transcription	Spleen	Spleen
28	chr17:19844400-19849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:19844600-19848600	Weak transcription	Fetal Lung	lung
30	chr17:19844600-19849800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:19844600-19849800	Weak transcription	HUVEC	blood vessel
32	chr17:19844600-19850000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:19844600-19850000	Weak transcription	NH-A	brain
34	chr17:19844600-19851400	Weak transcription	Brain Substantia Nigra	brain
35	chr17:19844600-19851600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:19844600-19851800	Weak transcription	Small Intestine	intestine
37	chr17:19844600-19859200	Weak transcription	NHDF-Ad	bronchial
38	chr17:19844800-19848800	Weak transcription	NHEK	skin
39	chr17:19844800-19849400	Weak transcription	HMEC	breast
40	chr17:19844800-19849600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:19844800-19851000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:19844800-19851600	Weak transcription	Fetal Heart	heart
43	chr17:19844800-19853000	Strong transcription	HepG2	liver
44	chr17:19844800-19859600	Weak transcription	HSMMtube	muscle
45	chr17:19844800-19861000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr17:19845200-19848800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:19845200-19848800	Weak transcription	Left Ventricle	heart
48	chr17:19845200-19848800	Weak transcription	Ovary	ovary
49	chr17:19845200-19849800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:19845200-19857200	Weak transcription	Fetal Kidney	kidney

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