Variant report

Variant	rs6493059
Chromosome Location	chr15:42977526-42977527
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10162939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10400824	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10518779	1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1058846	0.83[CEU][hapmap]
rs1197548	0.90[EUR][1000 genomes]
rs1197549	0.90[EUR][1000 genomes]
rs1197550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1197551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12102055	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs1212814	0.84[EUR][1000 genomes]
rs12324135	0.83[YRI][hapmap]
rs12594855	0.83[CEU][hapmap]
rs12902830	0.83[CEU][hapmap]
rs12905385	0.86[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs12906497	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs12911585	0.89[CEU][hapmap]
rs12912064	0.84[EUR][1000 genomes]
rs12914570	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap]
rs12917018	0.83[EUR][1000 genomes]
rs16957020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16957043	0.96[YRI][hapmap]
rs16957091	0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs16957104	0.84[EUR][1000 genomes]
rs16957168	0.81[ASW][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs1705356	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs17774047	0.83[CEU][hapmap]
rs1915241	0.81[EUR][1000 genomes]
rs1995939	0.85[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2136899	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2136900	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175370	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280048	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2305084	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305085	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2412740	0.86[EUR][1000 genomes]
rs28479391	0.87[EUR][1000 genomes]
rs28498538	0.90[ASN][1000 genomes]
rs28549876	0.83[EUR][1000 genomes]
rs28562951	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620320	0.85[ASN][1000 genomes]
rs28664781	0.83[ASN][1000 genomes]
rs28744617	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28798437	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28811114	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28823029	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099758	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs3106285	0.81[EUR][1000 genomes]
rs3106286	0.84[EUR][1000 genomes]
rs3199486	0.85[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs34603230	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3742987	0.85[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs3742993	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265781	0.83[EUR][1000 genomes]
rs4545789	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4924690	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4924691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924692	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4924694	1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs57298545	0.82[EUR][1000 genomes]
rs623271	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs6493063	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493066	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs672054	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs67391479	0.82[EUR][1000 genomes]
rs7163030	0.94[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7166373	0.89[CEU][hapmap]
rs7167392	0.80[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169009	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7169202	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs7175582	0.80[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7176860	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7182141	0.81[ASW][hapmap];0.80[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182515	1.00[JPT][hapmap]
rs8023524	0.84[CEU][hapmap];0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs8024902	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8026233	0.83[EUR][1000 genomes]
rs8027427	0.83[EUR][1000 genomes]
rs8028785	1.00[JPT][hapmap];0.92[MEX][hapmap]
rs8030587	0.83[CEU][hapmap]
rs8031218	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs8034664	0.83[EUR][1000 genomes]
rs8039711	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039765	0.89[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs8043472	1.00[CEU][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs9269	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938047	0.89[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs9783713	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9919994	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9920202	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6493059	CDAN1	cis	parietal	SCAN
rs6493059	BUB1B	cis	parietal	SCAN
rs6493059	CHAC1	cis	parietal	SCAN
rs6493059	SPTBN5	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42949800-42999200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr15:42950400-42990200	Strong transcription	Fetal Stomach	stomach
4	chr15:42951000-42995000	Strong transcription	Fetal Muscle Trunk	muscle
5	chr15:42952600-42979000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:42952600-42995600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:42952800-42996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:42953400-42992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42954600-42986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:42954800-42983000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:42955000-42990200	Strong transcription	Fetal Muscle Leg	muscle
12	chr15:42960000-42981800	Strong transcription	Primary T cells from cord blood	blood
13	chr15:42961000-42977600	Weak transcription	Small Intestine	intestine
14	chr15:42961200-42989200	Strong transcription	Ovary	ovary
15	chr15:42961400-42990800	Strong transcription	Colon Smooth Muscle	Colon
16	chr15:42961600-42989200	Weak transcription	Pancreas	Pancrea
17	chr15:42964200-42982400	Weak transcription	A549	lung
18	chr15:42964600-42979200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:42965000-42982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:42966000-42992800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:42966400-42978400	Weak transcription	Dnd41	blood
22	chr15:42966400-42988400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:42966400-42988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:42966600-42979400	Strong transcription	Spleen	Spleen
25	chr15:42966600-42979800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:42966600-42982400	Strong transcription	Fetal Brain Female	brain
27	chr15:42966600-42982800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr15:42966600-42988000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:42966600-42989200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:42966800-42987600	Strong transcription	Aorta	Aorta
31	chr15:42967200-42977600	Strong transcription	Primary B cells from cord blood	blood
32	chr15:42968400-42992200	Weak transcription	Fetal Brain Male	brain
33	chr15:42968600-42996800	Weak transcription	Liver	Liver
34	chr15:42968600-42999000	Weak transcription	HUVEC	blood vessel
35	chr15:42968800-42978000	Weak transcription	NH-A	brain
36	chr15:42969400-42988400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:42970200-42983400	Weak transcription	K562	blood
38	chr15:42970400-42979800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:42970600-42990200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:42970800-42986200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr15:42971400-42992600	Strong transcription	Adipose Nuclei	Adipose
42	chr15:42971600-42992400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:42972600-42983600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:42973000-42977800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:42973200-42979800	Weak transcription	NHEK	skin
46	chr15:42973200-42981000	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr15:42973200-42985600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr15:42973200-42991200	Strong transcription	Brain Germinal Matrix	brain
49	chr15:42973400-42977600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr15:42973400-42978200	Strong transcription	Gastric	stomach

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