Variant report

Variant	rs9300053
Chromosome Location	chr11:45878876-45878877
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	MAFK	chr11:45878493-45878932	IMR90	lung:	n/a	n/a
2	FOXP2	chr11:45878503-45878921	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr11:45878353-45880252	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:45878732-45878915	HepG2	liver:	n/a	n/a
5	GATA3	chr11:45878771-45878971	SH-SY5Y	brain:	n/a	n/a
6	CEBPB	chr11:45878554-45878927	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:45867823..45873583-chr11:45876186..45881298,10	MCF-7	breast:
2	chr11:45876957..45879799-chr11:46142347..46144267,2	MCF-7	breast:
3	chr11:45877056..45879214-chr5:147116551..147119032,2	MCF-7	breast:

Variant related genes	Relation type
CRY2	TF binding region
ENSG00000135365	Chromatin interaction
ENSG00000121671	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10838518	0.82[AMR][1000 genomes]
rs10838523	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12281069	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12281674	1.00[CEU][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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12284956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554338	0.89[JPT][hapmap];0.80[MEX][hapmap]
rs2037311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756038	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73466394	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73468311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73468335	0.96[AFR][1000 genomes]
rs73468338	0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9300053	DNALI1	trans	brain	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45869800-45883600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45870600-45879800	Weak transcription	Esophagus	oesophagus
3	chr11:45870800-45880800	Weak transcription	HMEC	breast
4	chr11:45872600-45880200	Weak transcription	Aorta	Aorta
5	chr11:45872800-45879000	Weak transcription	NH-A	brain
6	chr11:45873800-45879400	Strong transcription	Fetal Intestine Small	intestine
7	chr11:45874200-45904200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:45874600-45880000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:45874600-45880000	Weak transcription	Small Intestine	intestine
10	chr11:45875200-45882600	Genic enhancers	Liver	Liver
11	chr11:45875200-45905600	Strong transcription	Primary T cells from cord blood	blood
12	chr11:45875400-45893400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:45875800-45904200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr11:45876400-45904200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:45876600-45879400	Strong transcription	Fetal Thymus	thymus
16	chr11:45876600-45879600	Genic enhancers	Brain Anterior Caudate	brain
17	chr11:45876600-45882600	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr11:45876600-45882600	Enhancers	Right Atrium	heart
19	chr11:45876800-45879400	Strong transcription	Brain Germinal Matrix	brain
20	chr11:45876800-45879800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:45876800-45881800	Enhancers	Right Ventricle	heart
22	chr11:45876800-45882600	Genic enhancers	Fetal Muscle Leg	muscle
23	chr11:45876800-45882600	Genic enhancers	Fetal Stomach	stomach
24	chr11:45876800-45894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:45876800-45895600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:45876800-45895600	Strong transcription	Thymus	Thymus
27	chr11:45876800-45900200	Strong transcription	Primary B cells from cord blood	blood
28	chr11:45876800-45903600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr11:45876800-45904600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:45877000-45879400	Strong transcription	Placenta	Placenta
31	chr11:45877000-45880000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:45877000-45880000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:45877000-45881000	Genic enhancers	Brain Hippocampus Middle	brain
34	chr11:45877000-45885800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:45877000-45885800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
36	chr11:45877000-45885800	Strong transcription	Dnd41	blood
37	chr11:45877000-45885800	Strong transcription	GM12878-XiMat	blood
38	chr11:45877000-45885800	Strong transcription	K562	blood
39	chr11:45877000-45886000	Strong transcription	HepG2	liver
40	chr11:45877000-45893200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:45877000-45895600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:45877200-45879400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr11:45877200-45879400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:45877200-45879800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:45877200-45879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:45877200-45880600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:45877200-45881200	Genic enhancers	NHLF	lung
48	chr11:45877200-45881800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:45877200-45882600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:45877200-45883800	Genic enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links