Variant report

Variant	rs16957020
Chromosome Location	chr15:42964426-42964427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42960672..42962590-chr15:42963179..42966511,3	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10162939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10400824	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10518779	0.85[MEX][hapmap]
rs1058846	0.82[CEU][hapmap]
rs1197548	0.92[EUR][1000 genomes]
rs1197549	0.92[EUR][1000 genomes]
rs1197550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1197551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12102055	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1212814	0.85[EUR][1000 genomes]
rs12324135	0.80[YRI][hapmap]
rs12594855	0.82[CEU][hapmap]
rs12902830	0.82[CEU][hapmap]
rs12905385	0.86[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap]
rs12906497	0.83[EUR][1000 genomes]
rs12911585	0.88[CEU][hapmap]
rs12912064	0.83[EUR][1000 genomes]
rs12914570	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs12917018	0.83[EUR][1000 genomes]
rs16957043	0.86[YRI][hapmap]
rs16957091	0.82[EUR][1000 genomes]
rs16957104	0.82[EUR][1000 genomes]
rs16957168	0.81[ASW][hapmap];0.85[MEX][hapmap]
rs1705356	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17774047	0.82[CEU][hapmap]
rs1915241	0.81[EUR][1000 genomes]
rs1995939	0.84[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2136899	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[YRI][hapmap]
rs2136900	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2175370	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280048	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs2305084	1.00[CHB][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2305085	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2412740	0.86[EUR][1000 genomes]
rs28479391	0.88[EUR][1000 genomes]
rs28549876	0.83[EUR][1000 genomes]
rs28562951	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28744617	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28798437	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28811114	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28823029	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099758	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs3106285	0.83[EUR][1000 genomes]
rs3106286	0.86[EUR][1000 genomes]
rs3199486	0.84[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs34603230	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3742987	0.83[EUR][1000 genomes]
rs3742993	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs4265781	0.83[EUR][1000 genomes]
rs4545789	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924690	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4924691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924692	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924694	1.00[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs57298545	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs623271	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs6493059	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]
rs6493063	0.86[EUR][1000 genomes]
rs672054	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs67391479	0.81[EUR][1000 genomes]
rs7163030	0.94[CEU][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7166373	0.88[CEU][hapmap]
rs7167392	0.93[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs7169009	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7169202	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs7175582	0.95[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7182141	0.81[ASW][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs8023524	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs8024902	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026233	0.83[EUR][1000 genomes]
rs8027427	0.83[EUR][1000 genomes]
rs8028785	0.85[MEX][hapmap]
rs8030587	0.82[CEU][hapmap]
rs8031218	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs8034664	0.83[EUR][1000 genomes]
rs8039711	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8039765	0.88[CEU][hapmap];0.81[JPT][hapmap];0.84[MKK][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8043472	1.00[CEU][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs9269	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs938047	0.88[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9783713	0.89[EUR][1000 genomes]
rs9919994	0.84[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9920163	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]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16957020	BUB1B	cis	parietal	SCAN
rs16957020	CDAN1	cis	parietal	SCAN
rs16957020	CHAC1	cis	parietal	SCAN
rs16957020	SPTBN5	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

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	chr15:42925200-42966000	Weak transcription	NH-A	brain
5	chr15:42925200-42966800	Weak transcription	NHLF	lung
6	chr15:42928200-42973600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:42928200-42974000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:42931800-42968000	Weak transcription	HSMM	muscle
9	chr15:42932200-42966200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr15:42940400-42967800	Weak transcription	HepG2	liver
11	chr15:42942800-42967200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:42942800-42973600	Weak transcription	Psoas Muscle	Psoas
13	chr15:42945200-42973400	Weak transcription	Thymus	Thymus
14	chr15:42949800-42999200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:42950000-42969400	Weak transcription	K562	blood
16	chr15:42950400-42990200	Strong transcription	Fetal Stomach	stomach
17	chr15:42951000-42995000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:42952200-42973400	Weak transcription	Gastric	stomach
19	chr15:42952400-42970800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:42952600-42979000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:42952600-42995600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:42952800-42967000	Weak transcription	Right Ventricle	heart
23	chr15:42952800-42996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:42953200-42970000	Strong transcription	Adipose Nuclei	Adipose
25	chr15:42953200-42970200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr15:42953400-42992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:42953600-42967800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:42954000-42970000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:42954200-42973600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:42954400-42976200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:42954600-42986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:42954800-42983000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:42955000-42967000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:42955000-42990200	Strong transcription	Fetal Muscle Leg	muscle
35	chr15:42955200-42974000	Weak transcription	Esophagus	oesophagus
36	chr15:42956000-42967600	Weak transcription	Fetal Lung	lung
37	chr15:42956000-42976400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:42956200-42966400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:42956800-42964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:42956800-42973600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:42957000-42976200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:42958600-42966600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:42958800-42966200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:42958800-42966600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:42958800-42966800	Weak transcription	Aorta	Aorta
46	chr15:42958800-42967600	Weak transcription	HUVEC	blood vessel
47	chr15:42959000-42966000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:42959600-42966200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:42959800-42965200	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:42960000-42973400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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