Variant report

Variant	rs6482534
Chromosome Location	chr10:18868070-18868071
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10732437	1.00[ASN][1000 genomes]
rs10741086	1.00[CHB][hapmap]
rs10764566	0.81[MEX][hapmap];0.87[TSI][hapmap]
rs10764587	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10764661	1.00[ASN][1000 genomes]
rs10828835	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10828859	0.84[CEU][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10828970	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10829038	0.81[AMR][1000 genomes]
rs10829156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10829157	1.00[ASN][1000 genomes]
rs10829199	1.00[ASN][1000 genomes]
rs11015306	0.81[CEU][hapmap];0.93[YRI][hapmap]
rs11015307	0.84[CEU][hapmap];0.92[YRI][hapmap]
rs12359508	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12569760	0.81[AMR][1000 genomes]
rs12570585	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12765362	0.85[AMR][1000 genomes]
rs12772534	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12781038	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1352655	0.82[CEU][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs1880682	0.82[CEU][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs1917209	1.00[ASN][1000 genomes]
rs1917823	1.00[ASN][1000 genomes]
rs2691159	0.80[AMR][1000 genomes]
rs4338439	1.00[ASN][1000 genomes]
rs4456162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475829	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4475830	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484992	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4578284	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4606373	1.00[ASN][1000 genomes]
rs4634984	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636555	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748474	1.00[CHD][hapmap]
rs4748476	1.00[CHB][hapmap]
rs4748479	1.00[ASN][1000 genomes]
rs4748480	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4748489	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4748491	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4748493	1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748494	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4748495	0.92[CEU][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4748503	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs4748504	1.00[ASN][1000 genomes]
rs4748507	1.00[ASN][1000 genomes]
rs62636215	0.89[ASN][1000 genomes]
rs6482529	0.96[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6482545	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6482546	0.89[ASN][1000 genomes]
rs6482567	1.00[ASN][1000 genomes]
rs7068575	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7070695	0.80[CEU][hapmap];0.92[YRI][hapmap]
rs7071192	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7071897	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs7073651	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7075151	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7075304	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7075678	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7077786	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7080903	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7081435	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7081811	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7082094	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7082235	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7088214	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7090926	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7091578	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7092437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7093907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7095070	0.93[YRI][hapmap]
rs7095666	1.00[CHB][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs7098313	0.82[CEU][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap]
rs7098721	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099307	1.00[CHB][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs7099975	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7100884	1.00[ASN][1000 genomes]
rs7101269	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7895709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895775	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907153	0.86[TSI][hapmap];0.90[YRI][hapmap]
rs7908550	1.00[ASN][1000 genomes]
rs7909552	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7911922	1.00[ASN][1000 genomes]
rs7918933	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7921366	0.80[AMR][1000 genomes]
rs7923072	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8181345	1.00[ASN][1000 genomes]
rs9731044	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv1793653	chr10:18827828-18888369	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1794817	chr10:18827828-18888369	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv1811259	chr10:18827828-18888369	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv1840241	chr10:18827828-18888369	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv1841068	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1851495	chr10:18827828-18888369	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv1835982	chr10:18833550-18872699	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2757371	chr10:18835325-18906507	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2759736	chr10:18835325-18906507	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv466760	chr10:18839350-18905935	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv550044	chr10:18839350-18905935	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv1845973	chr10:18841795-18872699	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1793359	chr10:18841795-18872872	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1801825	chr10:18853581-18872699	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6482534	PTPLA	cis	cerebellum	SCAN
rs6482534	RP11-499P20.2	cis	lung	GTEx
rs6482534	NSUN6	cis	Nerve Tibial	GTEx
rs6482534	OLAH	cis	parietal	SCAN
rs6482534	NSUN6	cis	parietal	SCAN
rs6482534	NSUN6	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18842000-18868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:18842000-18869200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18842000-18886400	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:18844000-18871000	Weak transcription	Fetal Heart	heart
5	chr10:18846200-18899200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:18849000-18868600	Weak transcription	Gastric	stomach
8	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:18859600-18868600	Weak transcription	K562	blood
10	chr10:18861000-18883200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:18861800-18869000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:18862200-18868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:18862200-18894600	Weak transcription	HSMM	muscle
14	chr10:18862400-18878400	Strong transcription	Liver	Liver
15	chr10:18862600-18869200	Weak transcription	Fetal Brain Male	brain
16	chr10:18862600-18876600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:18863000-18894600	Weak transcription	A549	lung
18	chr10:18863000-18910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:18863200-18876400	Weak transcription	Spleen	Spleen
20	chr10:18863600-18875200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:18863800-18869000	Weak transcription	HepG2	liver
22	chr10:18863800-18869200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr10:18863800-18902200	Weak transcription	Brain Anterior Caudate	brain
24	chr10:18864800-18870800	Strong transcription	Ovary	ovary
25	chr10:18864800-18898000	Weak transcription	Fetal Kidney	kidney
26	chr10:18865000-18869600	Weak transcription	Brain Substantia Nigra	brain
27	chr10:18865200-18869200	Weak transcription	Brain Germinal Matrix	brain
28	chr10:18865600-18868600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr10:18865600-18869000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:18865600-18870600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:18865600-18885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:18865800-18869800	Weak transcription	Fetal Brain Female	brain
33	chr10:18866000-18868200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr10:18866000-18869000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:18866000-18869800	Weak transcription	Brain Hippocampus Middle	brain
36	chr10:18866200-18869000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:18866200-18869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:18866400-18868600	Weak transcription	Adipose Nuclei	Adipose
39	chr10:18866400-18869000	Weak transcription	Right Ventricle	heart
40	chr10:18866600-18869200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
41	chr10:18866600-18869400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr10:18866600-18899400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr10:18866800-18869200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
44	chr10:18866800-18870200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr10:18866800-18872000	Strong transcription	Left Ventricle	heart
46	chr10:18867000-18870600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:18867200-18869000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:18867200-18871400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr10:18867200-18871600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:18867200-18872400	Strong transcription	Rectal Mucosa Donor 29	rectum

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