Variant report

Variant	rs12772534
Chromosome Location	chr10:18866868-18866869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10741099	1.00[ASN][1000 genomes]
rs10764542	0.85[ASN][1000 genomes]
rs10764566	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs10764584	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828835	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828859	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10828879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828901	1.00[ASN][1000 genomes]
rs10828906	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10828970	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10829038	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10829133	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10829139	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10829140	1.00[ASN][1000 genomes]
rs11014830	1.00[ASN][1000 genomes]
rs11014852	1.00[ASN][1000 genomes]
rs11015263	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11015306	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs11015307	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11015411	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11015416	1.00[JPT][hapmap]
rs12359508	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12412484	0.83[AFR][1000 genomes]
rs12569760	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12570585	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12765362	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12771084	0.90[ASN][1000 genomes]
rs12776325	0.85[ASN][1000 genomes]
rs12781038	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352655	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17622920	1.00[JPT][hapmap]
rs1880682	0.82[CEU][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1968961	0.81[AFR][1000 genomes]
rs1971272	1.00[JPT][hapmap]
rs2691159	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4328135	0.91[ASN][1000 genomes]
rs4456162	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4475829	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4475830	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4484992	0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4578284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634984	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4636555	0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs4747353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4748474	1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs4748475	0.85[ASN][1000 genomes]
rs4748480	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4748489	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748491	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4748495	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748503	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4748508	1.00[ASN][1000 genomes]
rs6482516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6482529	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482534	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]
rs6482545	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7068575	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7070695	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7071192	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071897	0.82[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7073651	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7075151	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7075304	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7077692	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7078884	0.90[ASN][1000 genomes]
rs7080903	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081811	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082094	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084525	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7085332	0.90[ASN][1000 genomes]
rs7085587	0.90[ASN][1000 genomes]
rs7086034	0.90[ASN][1000 genomes]
rs7086911	0.91[ASN][1000 genomes]
rs7088214	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090293	0.90[ASN][1000 genomes]
rs7091578	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092437	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs7095070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7098313	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7098721	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7099307	0.82[MEX][hapmap]
rs7099975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101269	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7895235	1.00[ASN][1000 genomes]
rs7895709	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7895775	0.91[CEU][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7902450	1.00[JPT][hapmap]
rs7905730	1.00[JPT][hapmap]
rs7907153	0.86[LWK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs7917323	1.00[JPT][hapmap]
rs7920997	1.00[ASN][1000 genomes]
rs7921366	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12772534	ARL5B	cis	multi-tissue	Pritchard
rs12772534	RP11-499P20.2	cis	lung	GTEx
rs12772534	OLAH	cis	parietal	SCAN
rs12772534	PTPLA	cis	cerebellum	SCAN
rs12772534	NSUN6	cis	cerebellum	SCAN
rs12772534	NSUN6	cis	Nerve Tibial	GTEx
rs12772534	ARL5B	cis	lymphoblastoid	seeQTL
rs12772534	NSUN6	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18840800-18867200	Weak transcription	Fetal Thymus	thymus
2	chr10:18842000-18868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:18842000-18869200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr10:18842000-18886400	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:18844000-18871000	Weak transcription	Fetal Heart	heart
6	chr10:18846200-18899200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:18848400-18915800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:18849000-18868600	Weak transcription	Gastric	stomach
9	chr10:18849800-18910800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:18859600-18868600	Weak transcription	K562	blood
11	chr10:18861000-18883200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:18861600-18867000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:18861800-18869000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:18862200-18868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr10:18862200-18894600	Weak transcription	HSMM	muscle
16	chr10:18862400-18867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:18862400-18878400	Strong transcription	Liver	Liver
18	chr10:18862600-18869200	Weak transcription	Fetal Brain Male	brain
19	chr10:18862600-18876600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:18863000-18867000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr10:18863000-18894600	Weak transcription	A549	lung
22	chr10:18863000-18910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:18863200-18876400	Weak transcription	Spleen	Spleen
24	chr10:18863400-18867200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr10:18863600-18867000	Weak transcription	Placenta	Placenta
26	chr10:18863600-18875200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr10:18863800-18869000	Weak transcription	HepG2	liver
28	chr10:18863800-18869200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr10:18863800-18902200	Weak transcription	Brain Anterior Caudate	brain
30	chr10:18864200-18867200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:18864400-18867600	Strong transcription	Primary T cells from cord blood	blood
32	chr10:18864800-18867000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr10:18864800-18867400	Strong transcription	Primary B cells from cord blood	blood
34	chr10:18864800-18870800	Strong transcription	Ovary	ovary
35	chr10:18864800-18898000	Weak transcription	Fetal Kidney	kidney
36	chr10:18865000-18869600	Weak transcription	Brain Substantia Nigra	brain
37	chr10:18865200-18869200	Weak transcription	Brain Germinal Matrix	brain
38	chr10:18865400-18867800	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr10:18865600-18867800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
40	chr10:18865600-18867800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:18865600-18868600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr10:18865600-18869000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:18865600-18870600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:18865600-18885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr10:18865800-18867800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr10:18865800-18869800	Weak transcription	Fetal Brain Female	brain
47	chr10:18866000-18868200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
48	chr10:18866000-18869000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr10:18866000-18869800	Weak transcription	Brain Hippocampus Middle	brain
50	chr10:18866200-18867400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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