Variant report

Variant	rs17015226
Chromosome Location	chr1:209970096-209970097
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:209969683-209970493	PBDE	blood:	n/a	chr1:209970160-209970167 chr1:209970221-209970231
2	GATA2	chr1:209970020-209970310	SH-SY5Y	brain:	n/a	chr1:209970160-209970167 chr1:209970221-209970231
3	TAL1	chr1:209969890-209970352	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209970042..209972449-chr1:209978125..209979735,2	K562	blood:
2	chr1:209961943..209965694-chr1:209969094..209971510,3	K562	blood:
3	chr1:209968649..209970778-chr1:209979506..209982286,2	K562	blood:
4	chr1:209957462..209959935-chr1:209968588..209972462,3	K562	blood:
5	chr1:209969439..209971872-chr1:209988283..209991092,2	MCF-7	breast:
6	chr1:209967414..209971362-chr1:209996696..210001970,5	MCF-7	breast:

Variant related genes	Relation type
IRF6	TF binding region
ENSG00000117597	Chromatin interaction
ENSG00000162757	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1044516	0.86[ASW][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1073150	0.83[ASN][1000 genomes]
rs1160411	0.82[AFR][1000 genomes]
rs11803382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11805830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070337	0.90[AFR][1000 genomes]
rs12403599	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs1319072	0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1415543	0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs17015183	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17015218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015250	0.83[MKK][hapmap]
rs17015259	0.87[EUR][1000 genomes]
rs17015309	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[ASN][1000 genomes]
rs17015330	0.90[ASN][1000 genomes]
rs17015361	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17015379	0.82[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs17317411	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17389436	0.81[AMR][1000 genomes]
rs2005982	0.82[AFR][1000 genomes]
rs2013162	0.93[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2073485	0.93[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2073486	0.93[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2073487	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2179254	0.82[AFR][1000 genomes]
rs2235372	0.86[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2235373	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2235375	0.89[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs2236907	0.82[AFR][1000 genomes]
rs2236908	0.93[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap]
rs2236909	0.93[LWK][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2294408	0.81[AFR][1000 genomes]
rs2357229	0.94[YRI][hapmap]
rs2357230	0.88[ASN][1000 genomes]
rs3753518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41305104	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4556361	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs4844895	0.86[ASW][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs58637469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59100111	0.88[ASN][1000 genomes]
rs61747285	0.90[ASN][1000 genomes]
rs6540559	0.87[EUR][1000 genomes]
rs6540560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540561	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540563	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6540564	0.88[ASN][1000 genomes]
rs6685182	0.93[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs6694552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696825	0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6698154	0.90[ASN][1000 genomes]
rs73093853	0.83[ASN][1000 genomes]
rs742214	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs742215	0.80[ASW][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7511996	0.83[ASN][1000 genomes]
rs7522045	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7522250	0.87[EUR][1000 genomes]
rs7525951	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs7539638	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs7545542	0.96[LWK][hapmap];0.95[YRI][hapmap]
rs7550857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552506	0.96[LWK][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs764093	0.87[EUR][1000 genomes]
rs926346	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926347	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926348	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17015226	DYRK3	cis	parietal	SCAN
rs17015226	SYT14	cis	parietal	SCAN
rs17015226	LAMB3	cis	parietal	SCAN
rs17015226	TRAF3IP3	cis	Whole Blood	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
5	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
8	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
9	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
10	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr1:209962000-209972600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:209964600-209971600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:209965800-209970600	Strong transcription	Liver	Liver
21	chr1:209965800-209974600	Weak transcription	Small Intestine	intestine
22	chr1:209966000-209973000	Weak transcription	Left Ventricle	heart
23	chr1:209966000-209976200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
25	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:209966200-209970800	Weak transcription	Stomach Mucosa	stomach
27	chr1:209966200-209974600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:209966400-209971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:209966400-209971200	Strong transcription	HMEC	breast
30	chr1:209968000-209972000	Genic enhancers	Fetal Intestine Small	intestine
31	chr1:209968400-209971200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:209968400-209971800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:209968400-209975000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:209968600-209974200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:209968800-209971000	Strong transcription	NHEK	skin
36	chr1:209968800-209971600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:209968800-209974600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:209969000-209971000	Enhancers	Fetal Intestine Large	intestine
39	chr1:209969000-209971400	Weak transcription	Gastric	stomach
40	chr1:209969000-209972600	Weak transcription	Placenta	Placenta
41	chr1:209969000-209976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:209969000-209978600	Weak transcription	Lung	lung
43	chr1:209969400-209971400	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr1:209969600-209970600	Enhancers	Fetal Heart	heart
45	chr1:209969600-209971000	Genic enhancers	Esophagus	oesophagus
46	chr1:209969800-209970200	Enhancers	K562	blood
47	chr1:209970000-209971000	Weak transcription	Pancreas	Pancrea
48	chr1:209970000-209973200	Weak transcription	HUVEC	blood vessel
49	chr1:209970000-209975400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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