Variant report

Variant	rs10489344
Chromosome Location	chr1:210023787-210023788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:210021955..210024232-chr1:210027694..210029567,2	K562	blood:
2	chr1:210023442..210024326-chr1:210162412..210163363,3	MCF-7	breast:
3	chr1:210022253..210024519-chr1:210030671..210033538,2	K562	blood:
4	chr1:210013224..210015710-chr1:210023464..210025468,2	K562	blood:
5	chr1:210022782..210025213-chr1:210160452..210161959,2	K562	blood:
6	chr1:210017330..210020093-chr1:210023208..210026466,3	K562	blood:
7	chr1:209998850..210003154-chr1:210022698..210026040,4	K562	blood:
8	chr1:210023576..210025392-chr1:210424687..210427051,2	MCF-7	breast:
9	chr1:210023266..210025244-chr1:210030521..210032417,2	MCF-7	breast:
10	chr1:210020112..210021677-chr1:210023510..210025199,2	K562	blood:
11	chr1:210022631..210025512-chr1:210545924..210548792,3	K562	blood:
12	chr1:210011844..210014838-chr1:210022203..210024001,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction
ENSG00000117597	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10127937	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10218448	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582607	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11584081	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590807	1.00[JPT][hapmap]
rs11810091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12401430	0.90[ASN][1000 genomes]
rs12403006	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12404886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17317580	0.84[ASN][1000 genomes]
rs17389541	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs2013196	1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs28601717	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34743335	0.84[ASN][1000 genomes]
rs3753510	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753513	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766615	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274838	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4240837	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56071308	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56268268	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61820635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7544804	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7546104	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932334	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489344	IRF6	cis	cerebellum	SCAN
rs10489344	ETNK2	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:210004000-210027600	Strong transcription	K562	blood
15	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
18	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
20	chr1:210004200-210027600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:210004200-210027600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr1:210004200-210027600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr1:210004200-210027800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:210004200-210027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:210004200-210028000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:210004200-210028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:210004200-210028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
29	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
30	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
31	chr1:210004400-210029400	Strong transcription	Dnd41	blood
32	chr1:210004600-210028000	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:210004600-210028000	Strong transcription	GM12878-XiMat	blood
34	chr1:210006200-210025400	Strong transcription	Brain Hippocampus Middle	brain
35	chr1:210013200-210028800	Strong transcription	Fetal Intestine Large	intestine
36	chr1:210013400-210028800	Strong transcription	Liver	Liver
37	chr1:210013800-210028000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:210013800-210029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:210014400-210028800	Strong transcription	NHEK	skin
40	chr1:210014400-210029400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:210014600-210027600	Strong transcription	HSMM	muscle
42	chr1:210014600-210028200	Strong transcription	Hela-S3	cervix
43	chr1:210016000-210024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:210016800-210025800	Weak transcription	Colonic Mucosa	Colon
45	chr1:210017600-210024000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:210017600-210024200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:210017600-210024600	Weak transcription	Psoas Muscle	Psoas
48	chr1:210017600-210027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:210017600-210027800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:210017600-210027800	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links