Variant report

Variant	rs1427384
Chromosome Location	chr22:33257322-33257323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:33257234-33257570	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:33257133-33258848	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:33240885-33261662	ProgFib	skin:	n/a	n/a
4	POLR2A	chr22:33257200-33259031	HepG2	liver:	n/a	n/a
5	POLR2A	chr22:33257019-33257464	U87	brain:	n/a	n/a
6	FOSL2	chr22:33257217-33257726	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:33254453-33260989	IMR90	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32750950-32761732..22:33253287-33262063	Hela-S3	cervix:
2	22:32544939-32549151..22:33253287-33262063	Hela-S3	cervix:
3	22:32868055-32872511..22:33253287-33262063	Hela-S3	cervix:
4	22:31961151-31976153..22:33253287-33262063	K562	blood:
5	22:32920308-32927723..22:33253287-33262063	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000183531	TF binding region
ENSG00000271093	Chromatin interaction
ENSG00000205853	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000205856	Chromatin interaction
ENSG00000185666	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1065314	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427378	0.86[AMR][1000 genomes]
rs1427379	0.86[AMR][1000 genomes]
rs1427383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1543803	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1543804	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2040436	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2040437	0.87[ASW][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2040438	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2267184	0.87[ASW][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28456229	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899196	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749529	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749531	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749532	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5754315	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5754322	0.94[MEX][hapmap]
rs80689	0.83[MEX][hapmap]
rs933255	0.80[GIH][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes]
rs9621584	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1427384	GATSL3	cis	cerebellum	SCAN
rs1427384	SUGT1P1	trans	parietal	SCAN
rs1427384	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:92 , 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	chr22:33236200-33259000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:33237400-33282200	Weak transcription	Fetal Brain Female	brain
5	chr22:33238400-33259200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr22:33241600-33257800	Strong transcription	HepG2	liver
7	chr22:33241600-33258400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:33243400-33257600	Weak transcription	Fetal Brain Male	brain
9	chr22:33243400-33260200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:33244200-33262000	Weak transcription	Brain Germinal Matrix	brain
11	chr22:33244800-33257800	Strong transcription	NH-A	brain
12	chr22:33245000-33258800	Weak transcription	Pancreas	Pancrea
13	chr22:33245400-33258800	Strong transcription	HSMM	muscle
14	chr22:33245600-33265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr22:33245800-33264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:33247000-33258400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr22:33247400-33257600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr22:33247800-33260200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:33248000-33258400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr22:33248600-33257400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr22:33249400-33257800	Weak transcription	Small Intestine	intestine
22	chr22:33249400-33258600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr22:33249600-33259000	Strong transcription	Fetal Stomach	stomach
24	chr22:33249800-33258200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr22:33249800-33258800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:33249800-33262800	Weak transcription	Brain Angular Gyrus	brain
27	chr22:33250200-33257400	Genic enhancers	Right Ventricle	heart
28	chr22:33250400-33258800	Strong transcription	Osteobl	bone
29	chr22:33250600-33258800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:33250800-33258400	Strong transcription	Spleen	Spleen
31	chr22:33251000-33257400	Weak transcription	Esophagus	oesophagus
32	chr22:33251000-33257800	Strong transcription	NHDF-Ad	bronchial
33	chr22:33251400-33257600	Weak transcription	Brain Substantia Nigra	brain
34	chr22:33251400-33259000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr22:33251400-33259000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr22:33251400-33259400	Weak transcription	Right Atrium	heart
37	chr22:33251600-33258400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr22:33251600-33258600	Strong transcription	Adipose Nuclei	Adipose
39	chr22:33251600-33259000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr22:33252200-33257800	Strong transcription	NHLF	lung
41	chr22:33252400-33259200	Strong transcription	Left Ventricle	heart
42	chr22:33252400-33259200	Weak transcription	Psoas Muscle	Psoas
43	chr22:33252800-33259000	Strong transcription	Fetal Lung	lung
44	chr22:33253000-33258800	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr22:33253200-33257600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr22:33253200-33257600	Strong transcription	Liver	Liver
47	chr22:33253200-33257600	Strong transcription	Brain Cingulate Gyrus	brain
48	chr22:33253200-33257800	Strong transcription	Fetal Intestine Large	intestine
49	chr22:33253200-33258400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr22:33253200-33258400	Strong transcription	Aorta	Aorta

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