Variant report

Variant	rs5754315
Chromosome Location	chr22:33259064-33259065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:33258860-33259305	U87	brain:	n/a	n/a
2	POLR2A	chr22:33240885-33261662	ProgFib	skin:	n/a	n/a
3	POLR2A	chr22:33258901-33259565	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:33259025-33259206	HepG2	liver:	n/a	n/a
5	FOSL2	chr22:33258954-33259661	HepG2	liver:	n/a	n/a
6	POLR2A	chr22:33254453-33260989	IMR90	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32750950-32761732..22:33253287-33262063	Hela-S3	cervix:
2	chr22:33257978..33261996-chr22:33266633..33269916,3	K562	blood:
3	22:32544939-32549151..22:33253287-33262063	Hela-S3	cervix:
4	22:32868055-32872511..22:33253287-33262063	Hela-S3	cervix:
5	22:31961151-31976153..22:33253287-33262063	K562	blood:
6	22:32920308-32927723..22:33253287-33262063	Hela-S3	cervix:
7	chr22:33196558..33199719-chr22:33257750..33262273,4	MCF-7	breast:
8	chr22:33258265..33260703-chr22:33277216..33279656,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000183531	TF binding region
ENSG00000100225	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000205856	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000100234	Chromatin interaction
ENSG00000205853	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1065314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1427378	0.89[CEU][hapmap];0.85[GIH][hapmap];0.81[AMR][1000 genomes]
rs1427379	0.81[AMR][1000 genomes]
rs1427383	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1427384	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]
rs1543803	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1543804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2040435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040436	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2040437	0.93[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2040438	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2267184	0.93[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28456229	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2899196	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4608622	0.80[AMR][1000 genomes]
rs5749529	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5749531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5749532	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754319	0.80[AMR][1000 genomes]
rs5754321	0.80[AMR][1000 genomes]
rs5754322	0.94[MEX][hapmap]
rs80689	0.83[MEX][hapmap]
rs933255	0.94[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9621584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[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
rs5754315	GAL3ST1	cis	cerebellum	SCAN
rs5754315	SUGT1P1	trans	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33227000-33272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr22:33237400-33282200	Weak transcription	Fetal Brain Female	brain
3	chr22:33238400-33259200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr22:33243400-33260200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr22:33244200-33262000	Weak transcription	Brain Germinal Matrix	brain
6	chr22:33245600-33265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr22:33245800-33264800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:33247800-33260200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr22:33249800-33262800	Weak transcription	Brain Angular Gyrus	brain
10	chr22:33251400-33259400	Weak transcription	Right Atrium	heart
11	chr22:33252400-33259200	Strong transcription	Left Ventricle	heart
12	chr22:33252400-33259200	Weak transcription	Psoas Muscle	Psoas
13	chr22:33254600-33259400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:33255200-33263800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr22:33255800-33262000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr22:33256000-33259200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr22:33256000-33262200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr22:33256000-33263800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr22:33256000-33265200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr22:33256200-33259200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr22:33256200-33260000	Weak transcription	Fetal Kidney	kidney
22	chr22:33256200-33264800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr22:33256400-33259200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr22:33256400-33264400	Weak transcription	Brain Hippocampus Middle	brain
25	chr22:33256400-33269400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr22:33256800-33259400	Weak transcription	Brain Anterior Caudate	brain
27	chr22:33256800-33264800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr22:33257200-33259200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr22:33257200-33259400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr22:33257200-33262200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:33257600-33259400	Weak transcription	Liver	Liver
32	chr22:33257600-33259400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr22:33257600-33259400	Weak transcription	Ovary	ovary
34	chr22:33257600-33260000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:33257600-33261400	Weak transcription	Gastric	stomach
36	chr22:33257800-33259800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr22:33257800-33260400	Weak transcription	NH-A	brain
38	chr22:33257800-33261000	Weak transcription	NHLF	lung
39	chr22:33257800-33261200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr22:33257800-33264200	Weak transcription	NHDF-Ad	bronchial
41	chr22:33257800-33269600	Weak transcription	Fetal Intestine Small	intestine
42	chr22:33257800-33270000	Weak transcription	Fetal Intestine Large	intestine
43	chr22:33257800-33282000	Weak transcription	HepG2	liver
44	chr22:33258000-33262400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr22:33258200-33259400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr22:33258200-33260000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr22:33258200-33260400	Enhancers	Fetal Heart	heart
48	chr22:33258200-33266600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr22:33258400-33259400	Weak transcription	Lung	lung
50	chr22:33258400-33259400	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links