Variant report

Variant	rs1319072
Chromosome Location	chr1:210027654-210027655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210026504..210028571-chr1:210545991..210548661,2	K562	blood:
2	chr1:210026731..210029603-chr1:210060383..210062593,2	K562	blood:
3	chr1:210026504..210029493-chr1:210547161..210548663,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1044516	0.82[TSI][hapmap]
rs1073150	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11803382	0.90[JPT][hapmap]
rs1415543	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]
rs17015218	0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs17015226	0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs17015309	0.81[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17015330	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17015361	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17015379	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17317411	0.82[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap]
rs2073485	0.82[TSI][hapmap]
rs2205984	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206043	0.80[AMR][1000 genomes]
rs2235372	0.82[TSI][hapmap]
rs2357230	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35508116	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753518	0.91[JPT][hapmap]
rs4556361	0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4844895	0.82[TSI][hapmap]
rs59100111	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61747285	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6540560	0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6540563	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6540564	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6698154	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73093853	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742215	0.82[TSI][hapmap]
rs7511996	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7522045	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7525951	0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7539638	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7550857	0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

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
rs1319072	DYRK3	cis	parietal	SCAN
rs1319072	LAMB3	cis	parietal	SCAN
rs1319072	NFASC	cis	cerebellum	SCAN
rs1319072	SYT14	cis	parietal	SCAN
rs1319072	IRF6	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
15	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
17	chr1:210004200-210027800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:210004200-210027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:210004200-210028000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:210004200-210028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:210004200-210028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
23	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
25	chr1:210004400-210029400	Strong transcription	Dnd41	blood
26	chr1:210004600-210028000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:210004600-210028000	Strong transcription	GM12878-XiMat	blood
28	chr1:210013200-210028800	Strong transcription	Fetal Intestine Large	intestine
29	chr1:210013400-210028800	Strong transcription	Liver	Liver
30	chr1:210013800-210028000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:210013800-210029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:210014400-210028800	Strong transcription	NHEK	skin
33	chr1:210014400-210029400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:210014600-210028200	Strong transcription	Hela-S3	cervix
35	chr1:210017600-210027800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:210017600-210027800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:210017600-210041200	Weak transcription	Fetal Brain Male	brain
38	chr1:210018000-210032800	Weak transcription	Small Intestine	intestine
39	chr1:210018800-210029400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:210019000-210028600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:210019000-210033800	Weak transcription	Fetal Heart	heart
42	chr1:210019800-210027800	Strong transcription	NH-A	brain
43	chr1:210019800-210028800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:210019800-210030200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:210020000-210028000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:210020600-210029600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:210020800-210028200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:210020800-210028800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:210021000-210028000	Strong transcription	Placenta	Placenta
50	chr1:210021200-210028200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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