Variant report

Variant	rs5753469
Chromosome Location	chr22:31526811-31526812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31525510..31527221-chr22:31528778..31530795,2	K562	blood:
2	chr22:31365312..31368140-chr22:31526556..31529476,2	MCF-7	breast:
3	chr22:31520766..31523892-chr22:31525274..31529920,6	MCF-7	breast:
4	chr22:31518004..31520636-chr22:31524734..31527354,3	MCF-7	breast:
5	chr22:31501836..31504001-chr22:31525576..31528467,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185133	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000198832	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10854604	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1468411	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240431	0.89[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5753470	0.82[EUR][1000 genomes]
rs7291682	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7292168	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7292187	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs757873	0.94[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5753469	MTMR3	cis	parietal	SCAN
rs5753469	SFI1	cis	cerebellum	SCAN
rs5753469	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31519200-31527600	Weak transcription	Esophagus	oesophagus
2	chr22:31519200-31532600	Weak transcription	Ovary	ovary
3	chr22:31519400-31535400	Weak transcription	Lung	lung
4	chr22:31519600-31536000	Weak transcription	Brain Germinal Matrix	brain
5	chr22:31519800-31527600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr22:31519800-31528800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr22:31519800-31531600	Weak transcription	Brain Anterior Caudate	brain
8	chr22:31519800-31532000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr22:31519800-31532800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:31519800-31536000	Weak transcription	Gastric	stomach
11	chr22:31520000-31527600	Weak transcription	Stomach Mucosa	stomach
12	chr22:31520000-31531200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:31520000-31533200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr22:31520200-31535800	Weak transcription	Fetal Brain Female	brain
15	chr22:31520400-31538800	Weak transcription	Right Atrium	heart
16	chr22:31520800-31532000	Strong transcription	Fetal Intestine Small	intestine
17	chr22:31522800-31535200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr22:31523000-31530600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr22:31523400-31535600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr22:31523600-31528200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr22:31523600-31529200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr22:31523600-31530200	Weak transcription	Colonic Mucosa	Colon
23	chr22:31523800-31529000	Weak transcription	Fetal Stomach	stomach
24	chr22:31523800-31535200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:31524200-31527600	Weak transcription	Spleen	Spleen
26	chr22:31524200-31529000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr22:31524200-31530000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr22:31524400-31527600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr22:31524600-31527800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr22:31524600-31528800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr22:31524600-31529000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr22:31524600-31529000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr22:31524600-31533000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr22:31524600-31536000	Weak transcription	Right Ventricle	heart
35	chr22:31524800-31527800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr22:31524800-31529800	Weak transcription	Left Ventricle	heart
37	chr22:31524800-31530000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:31524800-31531400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr22:31524800-31532200	Weak transcription	Fetal Intestine Large	intestine
40	chr22:31524800-31533000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr22:31524800-31536400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr22:31526400-31527600	Enhancers	Hela-S3	cervix
43	chr22:31526400-31528000	Enhancers	K562	blood
44	chr22:31526600-31528600	Enhancers	HepG2	liver
45	chr22:31526800-31527000	Enhancers	Placenta	Placenta
46	chr22:31526800-31528200	Enhancers	Pancreas	Pancrea
47	chr22:31526800-31529600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:31526800-31529800	Strong transcription	Stomach Smooth Muscle	stomach

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