Variant report

Variant	rs5998058
Chromosome Location	chr22:32006408-32006409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:32006401-32006529	K562	blood:	n/a	n/a
2	POLR2A	chr22:32006379-32006423	HepG2	liver:	n/a	n/a
3	ZNF263	chr22:32006020-32007055	HEK293-T-REx	kidney:	n/a	chr22:32006766-32006775 chr22:32006158-32006167 chr22:32006763-32006772 chr22:32006159-32006180
4	POLR2A	chr22:32006080-32006445	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:32004632..32006593-chr22:32009952..32011895,2	K562	blood:
2	chr22:31998415..32000833-chr22:32004854..32006802,2	MCF-7	breast:
3	chr22:32004710..32007352-chr22:32026713..32029250,2	MCF-7	breast:
4	chr22:32006220..32009486-chr22:32009995..32012615,3	K562	blood:
5	chr22:32005385..32007517-chr22:32015792..32017582,2	MCF-7	breast:

Variant related genes	Relation type
SFI1	TF binding region
ENSG00000241878	Chromatin interaction
ENSG00000198089	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1018490	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1968023	0.83[CEU][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap]
rs2070274	0.87[ASN][1000 genomes]
rs2073281	0.81[CHB][hapmap]
rs2273249	0.80[CEU][hapmap]
rs2273251	0.80[CEU][hapmap]
rs28838399	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5749286	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs5749298	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs5753618	0.85[MEX][hapmap]
rs5753632	0.80[CEU][hapmap]
rs5753639	0.80[CEU][hapmap]
rs5753659	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs5753669	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs5753671	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs5753698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs5753723	0.83[CEU][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap]
rs5998067	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7284622	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs7285619	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs738657	0.80[CEU][hapmap]
rs8138525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8142355	1.00[LWK][hapmap]
rs9606843	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs9606848	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9609296	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs9609297	1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs9609304	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9609329	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914980	chr22:31966274-32024980	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv517534	chr22:31977594-32024980	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv829176	chr22:31998223-32029556	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5998058	SFI1	cis	Thyroid	GTEx
rs5998058	SFI1	cis	cerebellum	SCAN
rs5998058	PISD	cis	cerebellum	SCAN
rs5998058	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr22:31947800-32009600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr22:31949400-32014400	Weak transcription	Hela-S3	cervix
4	chr22:31957400-32016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:31976200-32014800	Weak transcription	A549	lung
6	chr22:31976400-32014800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr22:31976400-32019200	Weak transcription	Fetal Brain Male	brain
8	chr22:31985600-32014000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:31985800-32006600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr22:31985800-32010400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr22:31985800-32012400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:31985800-32014400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr22:31985800-32014800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:31990400-32014200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr22:31993200-32013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr22:31996000-32008400	Strong transcription	Primary T cells from cord blood	blood
17	chr22:31996200-32010000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr22:31996400-32010800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr22:31996600-32010600	Strong transcription	Thymus	Thymus
20	chr22:31996600-32011200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr22:31996600-32011800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr22:31996600-32012200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr22:31996600-32018200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr22:31996600-32020600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr22:31996800-32011600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:31997200-32012000	Strong transcription	Fetal Thymus	thymus
27	chr22:31997400-32010400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:31997600-32006600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr22:31997600-32008000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr22:31997600-32011400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr22:31998000-32008000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr22:31998400-32008000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr22:31998400-32015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr22:31998600-32022000	Weak transcription	Fetal Kidney	kidney
35	chr22:31998800-32006800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr22:31998800-32007000	Weak transcription	Liver	Liver
37	chr22:31998800-32010200	Weak transcription	Left Ventricle	heart
38	chr22:31998800-32012200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr22:31999000-32010000	Weak transcription	Right Ventricle	heart
40	chr22:31999000-32010200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr22:31999000-32010600	Weak transcription	Osteobl	bone
42	chr22:31999000-32011800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr22:31999000-32013800	Weak transcription	HMEC	breast
44	chr22:31999000-32014600	Weak transcription	NHDF-Ad	bronchial
45	chr22:31999200-32010600	Weak transcription	HUVEC	blood vessel
46	chr22:31999400-32006600	Weak transcription	Fetal Lung	lung
47	chr22:31999400-32008400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr22:31999400-32011400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr22:31999400-32011600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:31999400-32012800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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