Variant report

Variant	rs9420608
Chromosome Location	chr10:94800903-94800904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10509649	0.83[AMR][1000 genomes]
rs10748590	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882124	0.92[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs11187206	1.00[MEX][hapmap];0.84[TSI][hapmap]
rs11187243	0.87[AMR][1000 genomes]
rs11187247	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11187252	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11187257	0.85[AMR][1000 genomes]
rs11187258	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187259	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187263	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187264	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11187265	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1222605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263200	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354891	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12358168	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413378	0.83[AMR][1000 genomes]
rs12416051	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339820	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475366	0.91[AMR][1000 genomes]
rs17108036	0.82[AMR][1000 genomes]
rs17108042	0.83[AMR][1000 genomes]
rs17108043	0.83[AMR][1000 genomes]
rs17108050	0.83[AMR][1000 genomes]
rs1750741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2478233	0.89[AFR][1000 genomes]
rs2478238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486683	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486686	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486687	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35630863	0.89[ASN][1000 genomes]
rs4581378	0.89[ASN][1000 genomes]
rs4917898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919044	0.83[AMR][1000 genomes]
rs4919592	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55661575	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55853605	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55856996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58993699	0.89[ASN][1000 genomes]
rs59539045	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61568973	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61863079	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61863080	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61863087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073161	0.81[TSI][hapmap]
rs73317384	0.89[ASN][1000 genomes]
rs73319304	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73319347	0.89[ASN][1000 genomes]
rs73319398	0.89[ASN][1000 genomes]
rs7895700	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918909	0.92[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs835256	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835257	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835258	0.89[ASN][1000 genomes]
rs835260	0.89[ASN][1000 genomes]
rs835261	0.89[ASN][1000 genomes]
rs835262	0.89[ASN][1000 genomes]
rs835263	0.89[ASN][1000 genomes]
rs835265	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835269	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs835270	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835271	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835275	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835279	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs835280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][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]
rs844341	0.89[ASN][1000 genomes]
rs860669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9419761	0.89[ASN][1000 genomes]
rs9419763	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9419765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9419766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9420603	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9420607	0.89[ASN][1000 genomes]
rs9420610	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895898	chr10:94628274-94810665	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv522103	chr10:94660133-94810665	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv551942	chr10:94695617-94810665	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv7493	chr10:94794288-94802037	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9420608	CYP26C1	cis	cerebellum	SCAN
rs9420608	FLJ37201	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94713200-94819400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:94775400-94812800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr10:94780600-94801400	Weak transcription	Brain Anterior Caudate	brain
4	chr10:94781400-94807600	Weak transcription	Psoas Muscle	Psoas
5	chr10:94783400-94802800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr10:94785200-94819000	Weak transcription	Thymus	Thymus
7	chr10:94786400-94809200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:94787200-94817600	Weak transcription	Dnd41	blood
9	chr10:94787800-94802000	Weak transcription	Primary B cells from cord blood	blood
10	chr10:94787800-94814000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:94788000-94819000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:94788000-94819400	Weak transcription	Left Ventricle	heart
13	chr10:94788400-94803400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr10:94788400-94811000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:94788400-94815800	Weak transcription	Fetal Muscle Leg	muscle
16	chr10:94790800-94813800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr10:94792600-94819600	Weak transcription	Aorta	Aorta
18	chr10:94792600-94819800	Weak transcription	HSMMtube	muscle
19	chr10:94793000-94801600	Weak transcription	HUVEC	blood vessel
20	chr10:94793200-94811200	Weak transcription	HepG2	liver
21	chr10:94795000-94803200	Weak transcription	A549	lung
22	chr10:94795000-94810200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr10:94795600-94817800	Weak transcription	Fetal Intestine Small	intestine
24	chr10:94795800-94819600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:94798400-94804400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr10:94799200-94801000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:94799400-94801400	Strong transcription	Primary T cells from cord blood	blood
28	chr10:94799600-94803200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:94799800-94809200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:94799800-94817000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr10:94800000-94801000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr10:94800000-94803200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:94800000-94803200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:94800000-94803200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr10:94800000-94803200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr10:94800000-94803400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr10:94800000-94818400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr10:94800800-94809000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:94800800-94817600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr10:94800800-94818000	Weak transcription	Primary hematopoietic stem cells	blood

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