Variant report

Variant	rs1427378
Chromosome Location	chr22:33252041-33252042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:32860159-32865649..22:33247041-33253287	Hela-S3	cervix:
2	22:32920308-32927723..22:33247041-33253287	GM12878	blood:
3	22:32915608-32918105..22:33247041-33253287	K562	blood:
4	22:32764253-32784733..22:33247041-33253287	K562	blood:
5	22:32012966-32043914..22:33247041-33253287	K562	blood:
6	22:31836635-31847259..22:33247041-33253287	GM12878	blood:
7	22:33247041-33253287..22:33262063-33266567	GM12878	blood:
8	22:32750950-32761732..22:33247041-33253287	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000232218	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000243519	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000241954	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1065314	0.89[CEU][hapmap];0.82[GIH][hapmap];0.84[AMR][1000 genomes]
rs11703156	1.00[CHB][hapmap]
rs11703906	1.00[CHB][hapmap]
rs11704023	1.00[CHB][hapmap]
rs137501	1.00[CHB][hapmap]
rs1427377	1.00[CHB][hapmap]
rs1427379	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427383	0.85[AMR][1000 genomes]
rs1427384	0.86[AMR][1000 genomes]
rs1543803	0.81[AMR][1000 genomes]
rs1543804	0.81[AMR][1000 genomes]
rs2040435	0.80[GIH][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes]
rs2040436	0.85[AMR][1000 genomes]
rs2040437	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040438	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2267184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2267185	1.00[CHB][hapmap]
rs2413156	1.00[JPT][hapmap]
rs28456229	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899196	0.81[AMR][1000 genomes]
rs4999923	0.82[MEX][hapmap]
rs5749524	1.00[CHB][hapmap]
rs5749529	0.84[AMR][1000 genomes]
rs5749531	0.89[CEU][hapmap];0.85[GIH][hapmap];0.81[AMR][1000 genomes]
rs5754250	1.00[CHB][hapmap]
rs5754280	1.00[CHB][hapmap]
rs5754281	1.00[CHB][hapmap]
rs5754315	0.89[CEU][hapmap];0.85[GIH][hapmap];0.81[AMR][1000 genomes]
rs7289098	1.00[CHB][hapmap]
rs80689	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs933255	0.85[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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	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
2	nsv1059368	chr22:33249121-33268782	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1427378	SLC5A1	cis	cerebellum	SCAN
rs1427378	ARMCX6	trans	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33222600-33258800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr22:33227000-33272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr22:33227800-33252200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr22:33227800-33253200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr22:33228000-33252200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:33228000-33252600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr22:33236200-33253800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:33236200-33259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:33237400-33282200	Weak transcription	Fetal Brain Female	brain
10	chr22:33238400-33259200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr22:33241000-33252800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:33241600-33257800	Strong transcription	HepG2	liver
13	chr22:33241600-33258400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr22:33243200-33252800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr22:33243400-33257600	Weak transcription	Fetal Brain Male	brain
16	chr22:33243400-33260200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr22:33243600-33254000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr22:33243800-33252800	Weak transcription	Fetal Kidney	kidney
19	chr22:33243800-33255800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr22:33244200-33262000	Weak transcription	Brain Germinal Matrix	brain
21	chr22:33244400-33253600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr22:33244800-33257800	Strong transcription	NH-A	brain
23	chr22:33245000-33258800	Weak transcription	Pancreas	Pancrea
24	chr22:33245400-33258800	Strong transcription	HSMM	muscle
25	chr22:33245600-33265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr22:33245800-33264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr22:33246200-33253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr22:33247000-33258400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr22:33247400-33254000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:33247400-33257600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr22:33247800-33260200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr22:33248000-33258400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr22:33248200-33254200	Weak transcription	Colonic Mucosa	Colon
34	chr22:33248600-33257400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr22:33248800-33254200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr22:33248800-33255800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr22:33249000-33253800	Weak transcription	Gastric	stomach
38	chr22:33249200-33253200	Weak transcription	Liver	Liver
39	chr22:33249200-33253400	Weak transcription	Brain Hippocampus Middle	brain
40	chr22:33249200-33254000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr22:33249400-33253000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr22:33249400-33253200	Weak transcription	Aorta	Aorta
43	chr22:33249400-33253400	Weak transcription	Ovary	ovary
44	chr22:33249400-33254400	Weak transcription	Fetal Thymus	thymus
45	chr22:33249400-33257800	Weak transcription	Small Intestine	intestine
46	chr22:33249400-33258600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr22:33249600-33252400	Genic enhancers	Left Ventricle	heart
48	chr22:33249600-33253200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr22:33249600-33259000	Strong transcription	Fetal Stomach	stomach
50	chr22:33249800-33253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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