Variant report

Variant	rs12415807
Chromosome Location	chr10:94210809-94210810
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10786047	0.88[AFR][1000 genomes]
rs10882066	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882069	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882070	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882078	0.92[ASN][1000 genomes]
rs10882084	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs10882086	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs10882088	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs11186999	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187000	0.91[AFR][1000 genomes]
rs11187003	0.91[AFR][1000 genomes]
rs11187004	0.89[AFR][1000 genomes]
rs11187013	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11187016	0.82[ASN][1000 genomes]
rs11187018	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187034	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11187037	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187060	0.81[JPT][hapmap]
rs11187077	0.83[ASN][1000 genomes]
rs11187079	0.86[ASN][1000 genomes]
rs11187092	0.80[ASN][1000 genomes]
rs11187108	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs11187115	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11595187	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs11814555	0.85[AFR][1000 genomes]
rs12218324	0.80[ASN][1000 genomes]
rs12218329	0.92[ASN][1000 genomes]
rs12411517	0.90[ASN][1000 genomes]
rs12411873	0.80[ASN][1000 genomes]
rs12414433	0.86[ASN][1000 genomes]
rs12416180	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs17107539	0.83[TSI][hapmap]
rs17107734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1832197	0.81[JPT][hapmap]
rs1999763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs1999764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2275219	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs2297743	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2421940	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35118791	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35973022	0.81[EUR][1000 genomes]
rs3758503	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs3758505	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs3781237	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3781240	0.87[AFR][1000 genomes]
rs4646954	0.89[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs4646958	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4933231	0.91[AFR][1000 genomes]
rs4933232	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933725	0.86[AFR][1000 genomes]
rs4933726	0.91[AFR][1000 genomes]
rs4933728	0.89[ASN][1000 genomes]
rs4933731	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs57936176	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59415214	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6583817	0.82[ASN][1000 genomes]
rs6583820	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7068118	0.80[ASN][1000 genomes]
rs7068618	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7075073	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7078413	0.85[JPT][hapmap]
rs7079099	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7087153	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7089987	0.92[ASN][1000 genomes]
rs7093437	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097800	0.89[CHB][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs7895832	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7898114	0.91[ASN][1000 genomes]
rs7898862	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900584	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs7910605	0.96[GIH][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs7910977	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7911558	0.87[AFR][1000 genomes]
rs7916460	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv508600	chr10:94115025-94231917	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12415807	CYP26A1	cis	cerebellum	SCAN
rs12415807	SLC16A12	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94191000-94211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr10:94200000-94214200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:94201600-94214400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:94204600-94211400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:94204600-94211800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr10:94205200-94211800	Weak transcription	Placenta	Placenta
7	chr10:94205200-94212800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:94205200-94214400	Weak transcription	Right Ventricle	heart
9	chr10:94205600-94214400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:94205800-94214400	Weak transcription	Fetal Stomach	stomach
11	chr10:94205800-94221800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:94206200-94211600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:94206200-94211800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:94206200-94212200	Weak transcription	HMEC	breast
15	chr10:94206200-94214200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:94206200-94214400	Weak transcription	K562	blood
17	chr10:94206400-94211400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:94206400-94213200	Weak transcription	HUVEC	blood vessel
19	chr10:94206400-94214200	Weak transcription	Fetal Intestine Large	intestine
20	chr10:94206400-94214400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr10:94206400-94222600	Weak transcription	HSMMtube	muscle
22	chr10:94206600-94212000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:94206600-94212000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr10:94207000-94212200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:94207000-94212400	Weak transcription	Ovary	ovary
26	chr10:94207000-94214400	Weak transcription	Gastric	stomach
27	chr10:94207200-94214400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr10:94207600-94213200	Weak transcription	Hela-S3	cervix
29	chr10:94207800-94211200	Weak transcription	Osteobl	bone
30	chr10:94207800-94211400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr10:94207800-94211600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr10:94207800-94212000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr10:94207800-94213400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:94207800-94214000	Weak transcription	Left Ventricle	heart
35	chr10:94207800-94222000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr10:94208000-94211400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr10:94208000-94211400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr10:94208000-94211400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr10:94208000-94211800	Weak transcription	Primary T cells from cord blood	blood
40	chr10:94208000-94212000	Weak transcription	Primary B cells from cord blood	blood
41	chr10:94208000-94212000	Weak transcription	Dnd41	blood
42	chr10:94208000-94212200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr10:94208000-94213200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:94208000-94214000	Weak transcription	Brain Anterior Caudate	brain
45	chr10:94208000-94214200	Weak transcription	Fetal Lung	lung
46	chr10:94208000-94215600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr10:94208000-94219800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:94208000-94222400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr10:94208000-94223600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr10:94208000-94224000	Weak transcription	Fetal Kidney	kidney

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