Variant report

Variant	rs9536048
Chromosome Location	chr13:52958788-52958789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52955682..52957197-chr13:52957255..52959376,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1056335	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11148252	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11618716	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11620062	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs1327323	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap]
rs13431	0.93[ASN][1000 genomes]
rs1815348	0.90[CHB][hapmap]
rs1815669	0.94[ASN][1000 genomes]
rs3803262	0.90[ASN][1000 genomes]
rs3803264	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.99[ASN][1000 genomes]
rs3886077	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs3892337	0.86[CHB][hapmap]
rs4286007	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4545703	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs4884320	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4884354	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4884452	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4885953	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4886018	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4886077	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs61958050	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6561665	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[ASN][1000 genomes]
rs7321964	0.86[CHB][hapmap]
rs7323666	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7333451	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7336679	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7399631	0.91[ASN][1000 genomes]
rs7983971	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs7985262	0.93[ASN][1000 genomes]
rs7987115	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7990581	0.86[CHB][hapmap]
rs7993748	0.90[CHB][hapmap]
rs8001624	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9379	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9526913	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9526914	0.98[ASN][1000 genomes]
rs9535895	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9536046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs9536052	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs9536066	0.86[CHB][hapmap]
rs9536069	0.90[ASN][1000 genomes]
rs9536079	0.86[CHB][hapmap]
rs9568728	0.93[ASN][1000 genomes]
rs9568732	0.86[CHB][hapmap]
rs9568734	0.80[CHB][hapmap]
rs9596643	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs9596648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9596651	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9536048	LECT1	cis	parietal	SCAN
rs9536048	CKAP2	cis	cerebellum	SCAN
rs9536048	VPS36	cis	cerebellum	SCAN
rs9536048	CKAP2	cis	Artery Tibial	GTEx
rs9536048	CKAP2	cis	parietal	SCAN
rs9536048	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9536048	ATP7B	cis	cerebellum	SCAN
rs9536048	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52946000-52969600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr13:52946200-52979200	Weak transcription	A549	lung
3	chr13:52947800-52968000	Weak transcription	NHDF-Ad	bronchial
4	chr13:52949800-52979000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:52951200-52961400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:52952000-52964400	Weak transcription	Brain Hippocampus Middle	brain
7	chr13:52952600-52963400	Weak transcription	Fetal Intestine Large	intestine
8	chr13:52952600-52969200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:52952800-52959200	Weak transcription	Left Ventricle	heart
10	chr13:52952800-52960200	Weak transcription	Aorta	Aorta
11	chr13:52952800-52967000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr13:52952800-52968000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr13:52952800-52969000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:52952800-52969200	Weak transcription	Fetal Brain Female	brain
15	chr13:52952800-52969200	Weak transcription	Spleen	Spleen
16	chr13:52952800-52969200	Weak transcription	NHEK	skin
17	chr13:52952800-52969600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:52952800-52969600	Weak transcription	NHLF	lung
19	chr13:52952800-52971400	Weak transcription	Right Ventricle	heart
20	chr13:52953000-52961200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:52953000-52961400	Weak transcription	Fetal Intestine Small	intestine
22	chr13:52953000-52964400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr13:52953000-52968000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:52953000-52970000	Weak transcription	Ovary	ovary
25	chr13:52955600-52969600	Weak transcription	Lung	lung
26	chr13:52955800-52961800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:52956200-52978200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr13:52956600-52960800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:52956600-52961000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr13:52956600-52961000	Strong transcription	Fetal Muscle Leg	muscle
31	chr13:52957000-52959600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr13:52957200-52960400	Strong transcription	HMEC	breast
33	chr13:52957400-52960400	Strong transcription	HSMM	muscle
34	chr13:52957400-52967000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr13:52957800-52969000	Weak transcription	Adipose Nuclei	Adipose
36	chr13:52957800-52969600	Weak transcription	Fetal Stomach	stomach
37	chr13:52958000-52959800	Strong transcription	HUVEC	blood vessel
38	chr13:52958000-52960200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr13:52958000-52969200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:52958000-52969200	Weak transcription	HSMMtube	muscle
41	chr13:52958000-52969400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:52958000-52970800	Weak transcription	Fetal Lung	lung
43	chr13:52958400-52960400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:52958400-52960800	Strong transcription	Osteobl	bone
45	chr13:52958600-52960600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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