Variant report

Variant	rs9920163
Chromosome Location	chr15:42942381-42942382
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42942192..42943864-chr15:42944644..42946826,2	K562	blood:
2	chr15:42940947..42942447-chr19:4057604..4059957,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10162939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10400824	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10518779	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs1058846	0.83[CEU][hapmap]
rs1197548	0.92[EUR][1000 genomes]
rs1197549	0.92[EUR][1000 genomes]
rs1197550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12102055	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1212814	0.84[EUR][1000 genomes]
rs12324135	0.96[YRI][hapmap]
rs12594855	0.83[CEU][hapmap]
rs12902830	0.83[CEU][hapmap]
rs12905385	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs12906497	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs12911585	0.89[CEU][hapmap]
rs12912064	0.82[EUR][1000 genomes]
rs12914570	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap]
rs12917018	0.81[EUR][1000 genomes]
rs16957020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16957043	0.90[YRI][hapmap]
rs16957091	0.81[EUR][1000 genomes]
rs16957104	0.81[EUR][1000 genomes]
rs16957168	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs1705356	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17774047	0.83[CEU][hapmap]
rs1995939	0.85[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2136899	0.81[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2136900	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2175370	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280048	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs2305084	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305085	1.00[CHB][hapmap]
rs2412740	0.84[EUR][1000 genomes]
rs28479391	0.87[EUR][1000 genomes]
rs28549876	0.81[EUR][1000 genomes]
rs28562951	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28664781	0.95[ASN][1000 genomes]
rs28744617	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28798437	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28811114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28823029	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3099758	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs3106285	0.83[EUR][1000 genomes]
rs3106286	0.84[EUR][1000 genomes]
rs3199486	0.85[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs34603230	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742987	0.82[EUR][1000 genomes]
rs3742993	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs4265781	0.81[EUR][1000 genomes]
rs4545789	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924690	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4924691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924692	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924694	1.00[CHB][hapmap];0.95[GIH][hapmap]
rs57298545	0.82[EUR][1000 genomes]
rs623271	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs6493059	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]
rs6493063	0.84[EUR][1000 genomes]
rs672054	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7163030	0.94[CEU][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166373	0.89[CEU][hapmap]
rs7167392	0.80[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7169009	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7169202	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs7175582	0.80[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7176860	0.88[ASN][1000 genomes]
rs7182141	0.80[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7182515	0.90[JPT][hapmap]
rs8023524	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs8024902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8026233	0.81[EUR][1000 genomes]
rs8027427	0.81[EUR][1000 genomes]
rs8028785	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs8030587	0.83[CEU][hapmap]
rs8031218	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs8034664	0.82[EUR][1000 genomes]
rs8039711	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039765	0.89[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes]
rs8043472	1.00[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs9269	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs938047	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9783713	0.88[EUR][1000 genomes]
rs9919994	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9920163	BUB1B	cis	parietal	SCAN
rs9920163	CHAC1	cis	parietal	SCAN
rs9920163	SPTBN5	cis	cerebellum	SCAN
rs9920163	CDAN1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42898000-42967800	Weak transcription	Fetal Intestine Small	intestine
2	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
3	chr15:42909600-42966400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:42923000-42958200	Weak transcription	Hela-S3	cervix
5	chr15:42924400-42944600	Weak transcription	Thymus	Thymus
6	chr15:42925200-42966000	Weak transcription	NH-A	brain
7	chr15:42925200-42966800	Weak transcription	NHLF	lung
8	chr15:42925600-42961000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:42926400-42947200	Weak transcription	Fetal Brain Male	brain
10	chr15:42928200-42973600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:42928200-42974000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:42930600-42964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:42930800-42957400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:42931000-42942400	Weak transcription	HMEC	breast
15	chr15:42931200-42949800	Weak transcription	Fetal Heart	heart
16	chr15:42931200-42954600	Weak transcription	Placenta	Placenta
17	chr15:42931200-42963400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:42931400-42942400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:42931400-42944600	Weak transcription	NHDF-Ad	bronchial
20	chr15:42931400-42955800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:42931600-42942400	Weak transcription	Brain Substantia Nigra	brain
22	chr15:42931600-42942600	Weak transcription	Spleen	Spleen
23	chr15:42931600-42944000	Weak transcription	Left Ventricle	heart
24	chr15:42931600-42948800	Weak transcription	Brain Anterior Caudate	brain
25	chr15:42931600-42953600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:42931600-42955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:42931800-42955000	Weak transcription	Fetal Lung	lung
28	chr15:42931800-42955000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:42931800-42955600	Weak transcription	Lung	lung
30	chr15:42931800-42957200	Weak transcription	Primary B cells from cord blood	blood
31	chr15:42931800-42958200	Weak transcription	Brain Angular Gyrus	brain
32	chr15:42931800-42968000	Weak transcription	HSMM	muscle
33	chr15:42932000-42944600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:42932000-42944600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:42932000-42944600	Weak transcription	Adipose Nuclei	Adipose
36	chr15:42932000-42958400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:42932200-42944600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:42932200-42966200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr15:42932400-42942400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:42932400-42942600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:42932400-42943800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:42932400-42960000	Weak transcription	Primary T cells from cord blood	blood
43	chr15:42932600-42944400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:42932600-42944600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:42932600-42953200	Weak transcription	Fetal Intestine Large	intestine
46	chr15:42932600-42955400	Weak transcription	Aorta	Aorta
47	chr15:42932800-42942600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:42932800-42953000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:42932800-42954000	Weak transcription	Brain Germinal Matrix	brain
50	chr15:42933400-42943400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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