Variant report

Variant	rs3099758
Chromosome Location	chr15:42927984-42927985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10162939	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs10400824	0.93[EUR][1000 genomes]
rs1058846	0.83[CEU][hapmap]
rs1197548	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197549	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1197550	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs1197551	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs12102055	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1212814	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12594855	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12594858	1.00[YRI][hapmap]
rs12902830	0.83[CEU][hapmap]
rs12905385	0.84[CEU][hapmap]
rs12906497	0.80[CEU][hapmap]
rs12911585	0.89[CEU][hapmap]
rs12914570	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12917018	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs12917189	0.84[GIH][hapmap];0.85[MEX][hapmap]
rs16957020	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs16957091	0.93[GIH][hapmap];0.93[MEX][hapmap]
rs16957168	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs1705356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774047	0.83[CEU][hapmap]
rs1995939	0.85[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2136899	0.90[JPT][hapmap]
rs2136900	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2175370	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2280048	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2305084	0.80[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2412740	0.82[EUR][1000 genomes]
rs28479391	0.82[EUR][1000 genomes]
rs28562951	0.84[EUR][1000 genomes]
rs28744617	0.85[EUR][1000 genomes]
rs28798437	0.93[EUR][1000 genomes]
rs28811114	0.92[EUR][1000 genomes]
rs28823029	0.92[EUR][1000 genomes]
rs3106285	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3106286	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3199486	0.85[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs34070722	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742987	0.91[GIH][hapmap];0.93[MEX][hapmap];0.80[EUR][1000 genomes]
rs3742988	0.91[GIH][hapmap];0.85[MEX][hapmap]
rs3742993	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs4545789	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4924690	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924691	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs4924692	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4994112	0.91[GIH][hapmap];0.85[MEX][hapmap]
rs57298545	0.85[ASN][1000 genomes]
rs623271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493059	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs6493060	0.86[GIH][hapmap];0.85[MEX][hapmap]
rs6493061	0.87[GIH][hapmap];0.85[MEX][hapmap]
rs672054	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7163030	0.94[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs7166373	0.89[CEU][hapmap]
rs7166775	0.93[MEX][hapmap]
rs7167392	0.80[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs7169009	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs7169202	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7175582	0.80[CEU][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs7182141	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs7182515	0.90[JPT][hapmap]
rs731984	0.91[GIH][hapmap]
rs8023524	0.84[CEU][hapmap]
rs8024902	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs8030587	0.83[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap]
rs8031218	0.83[CEU][hapmap]
rs8034447	0.91[GIH][hapmap];0.85[MEX][hapmap]
rs8039711	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs8039765	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8043472	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs9269	0.89[CEU][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs938047	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9783713	0.83[EUR][1000 genomes]
rs9919994	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]
rs9920163	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3099758	CDAN1	cis	parietal	SCAN
rs3099758	BUB1B	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42874800-42929800	Weak transcription	Fetal Brain Female	brain
2	chr15:42897800-42930200	Weak transcription	HSMM	muscle
3	chr15:42898000-42967800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:42898400-42932800	Weak transcription	Esophagus	oesophagus
5	chr15:42898600-42929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:42900600-42928000	Weak transcription	Placenta	Placenta
7	chr15:42900600-42930000	Weak transcription	HMEC	breast
8	chr15:42900800-42929800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:42901400-42928400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:42901400-42929800	Weak transcription	Brain Angular Gyrus	brain
11	chr15:42901600-42930000	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:42901600-42930400	Weak transcription	Primary B cells from cord blood	blood
13	chr15:42903200-42931000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:42904000-42930200	Weak transcription	Right Ventricle	heart
15	chr15:42904200-42929800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:42904600-42930200	Weak transcription	Aorta	Aorta
17	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
18	chr15:42909600-42966400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:42910200-42929800	Weak transcription	Fetal Heart	heart
20	chr15:42912200-42929400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:42912800-42933200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:42914800-42930200	Weak transcription	Spleen	Spleen
23	chr15:42915200-42940000	Weak transcription	HepG2	liver
24	chr15:42921200-42929600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:42921400-42930200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:42921600-42929400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:42921600-42929800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:42921800-42928000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:42922000-42929400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:42922000-42932200	Weak transcription	K562	blood
31	chr15:42922000-42932800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:42922600-42930000	Weak transcription	NHDF-Ad	bronchial
33	chr15:42923000-42958200	Weak transcription	Hela-S3	cervix
34	chr15:42923800-42928000	Weak transcription	Lung	lung
35	chr15:42923800-42929800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:42924200-42931800	Weak transcription	HUVEC	blood vessel
37	chr15:42924400-42930000	Weak transcription	Brain Substantia Nigra	brain
38	chr15:42924400-42944600	Weak transcription	Thymus	Thymus
39	chr15:42924600-42928400	Weak transcription	Brain Germinal Matrix	brain
40	chr15:42924600-42930200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:42925000-42930000	Weak transcription	Primary T cells from cord blood	blood
42	chr15:42925000-42934400	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:42925000-42936000	Strong transcription	Fetal Stomach	stomach
44	chr15:42925200-42966000	Weak transcription	NH-A	brain
45	chr15:42925200-42966800	Weak transcription	NHLF	lung
46	chr15:42925400-42933400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:42925600-42929600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:42925600-42933400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:42925600-42961000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:42925800-42929800	Weak transcription	Brain Anterior Caudate	brain

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