Variant report

Variant	rs1415543
Chromosome Location	chr1:210016709-210016710
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210002486..210004655-chr1:210015863..210018980,3	K562	blood:
2	chr1:210013134..210015297-chr1:210015334..210016839,2	MCF-7	breast:
3	chr1:210016233..210018147-chr1:210024222..210027045,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1044516	0.86[TSI][hapmap]
rs1073150	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803382	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11805830	0.86[ASN][1000 genomes]
rs1319072	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1319435	0.88[AMR][1000 genomes]
rs17015218	0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs17015224	0.83[ASN][1000 genomes]
rs17015226	0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs17015309	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015330	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17015361	1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015379	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17317411	0.86[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2073485	0.86[TSI][hapmap]
rs2205984	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2235372	0.86[TSI][hapmap]
rs2357230	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35508116	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3753518	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4556361	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844895	0.86[TSI][hapmap]
rs55871867	0.86[AMR][1000 genomes]
rs58637469	0.83[ASN][1000 genomes]
rs59100111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61747285	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540560	0.90[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs6540561	0.86[ASN][1000 genomes]
rs6540563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540564	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6694552	0.81[ASN][1000 genomes]
rs6696825	0.82[TSI][hapmap]
rs6698154	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73093853	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs735694	0.88[AMR][1000 genomes]
rs742215	0.86[TSI][hapmap]
rs7511996	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522045	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540237	0.88[AMR][1000 genomes]
rs7550857	0.90[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs7551944	0.88[AMR][1000 genomes]
rs926346	0.83[ASN][1000 genomes]
rs926347	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1415543	LAMB3	cis	parietal	SCAN
rs1415543	SYT14	cis	parietal	SCAN
rs1415543	IRF6	cis	cerebellum	SCAN
rs1415543	DYRK3	cis	parietal	SCAN
rs1415543	NFASC	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
2	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:210003200-210017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:210004000-210019000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:210004000-210019000	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:210004000-210027600	Strong transcription	K562	blood
19	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
22	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
24	chr1:210004200-210017600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:210004200-210018200	Strong transcription	Brain Substantia Nigra	brain
26	chr1:210004200-210018600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:210004200-210018600	Strong transcription	Fetal Lung	lung
28	chr1:210004200-210018600	Strong transcription	Left Ventricle	heart
29	chr1:210004200-210018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:210004200-210018800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:210004200-210019000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:210004200-210019000	Strong transcription	Brain Anterior Caudate	brain
33	chr1:210004200-210019400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:210004200-210019400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:210004200-210020200	Strong transcription	Brain Angular Gyrus	brain
36	chr1:210004200-210020200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:210004200-210022000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:210004200-210027600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:210004200-210027600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:210004200-210027600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:210004200-210027800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:210004200-210027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:210004200-210028000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:210004200-210028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:210004200-210028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
47	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
49	chr1:210004400-210017400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:210004400-210019800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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