Variant report

Variant	rs1427385
Chromosome Location	chr22:33244314-33244315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33244019..33245716-chr22:33248681..33250493,2	MCF-7	breast:
2	22:31998728-32011472..22:33242943-33247041	GM12878	blood:

Variant related genes	Relation type
ENSG00000198089	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs137487	0.85[GIH][hapmap]
rs2071947	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2267183	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283883	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2283884	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs2283885	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs5754312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv3599	chr22:33230106-33274789	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1427385	C22orf42	cis	parietal	SCAN
rs1427385	SEC14L2	cis	cerebellum	SCAN
rs1427385	ARMCX6	trans	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33217800-33248600	Weak transcription	Gastric	stomach
2	chr22:33222600-33258800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr22:33227000-33272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr22:33227600-33248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr22:33227600-33249400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr22:33227800-33252200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr22:33227800-33253200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr22:33228000-33245000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:33228000-33252200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:33228000-33252600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:33231200-33245400	Weak transcription	NHLF	lung
12	chr22:33232400-33245600	Weak transcription	HSMMtube	muscle
13	chr22:33235600-33245200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:33236200-33245600	Weak transcription	Aorta	Aorta
15	chr22:33236200-33253800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:33236200-33259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:33237000-33245600	Weak transcription	Fetal Intestine Small	intestine
18	chr22:33237400-33245600	Weak transcription	Fetal Intestine Large	intestine
19	chr22:33237400-33282200	Weak transcription	Fetal Brain Female	brain
20	chr22:33238400-33259200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr22:33238800-33244800	Weak transcription	NH-A	brain
22	chr22:33239000-33245600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:33239000-33246200	Weak transcription	NHDF-Ad	bronchial
24	chr22:33239000-33248800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr22:33239200-33248400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:33239600-33245600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr22:33239800-33245400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr22:33239800-33245400	Weak transcription	Spleen	Spleen
29	chr22:33240200-33245000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr22:33240200-33245600	Weak transcription	Brain Angular Gyrus	brain
31	chr22:33240800-33244800	Enhancers	Adipose Nuclei	Adipose
32	chr22:33241000-33252800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr22:33241200-33245400	Enhancers	Right Ventricle	heart
34	chr22:33241400-33244800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr22:33241400-33251400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr22:33241600-33251600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr22:33241600-33257800	Strong transcription	HepG2	liver
38	chr22:33241600-33258400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr22:33241800-33246400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr22:33242400-33245000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr22:33242400-33245400	Enhancers	Placenta	Placenta
42	chr22:33242400-33246200	Weak transcription	Colonic Mucosa	Colon
43	chr22:33242800-33244800	Enhancers	Fetal Heart	heart
44	chr22:33243200-33246000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr22:33243200-33246200	Strong transcription	Osteobl	bone
46	chr22:33243200-33252800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr22:33243400-33244400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr22:33243400-33244800	Weak transcription	Brain Substantia Nigra	brain
49	chr22:33243400-33244800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr22:33243400-33244800	Weak transcription	Lung	lung

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