Variant report

Variant	rs7291918
Chromosome Location	chr22:32008039-32008040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:32007661-32008042	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:32008021..32010737-chr22:32022618..32024504,2	MCF-7	breast:
2	chr22:32000648..32004011-chr22:32006419..32009000,3	K562	blood:
3	chr22:32006220..32009486-chr22:32009995..32012615,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DRG1-3	chr22:32007985-32008428	NONHSAT084904

No data

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

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044085	0.90[JPT][hapmap]
rs10775716	0.89[ASN][1000 genomes]
rs12170867	0.90[JPT][hapmap]
rs12171042	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12627933	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs131233	0.82[YRI][hapmap]
rs131250	0.83[MEX][hapmap]
rs140078	0.83[ASW][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs140081	0.83[ASW][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs14034	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1543416	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs2006771	0.98[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs2024747	0.85[JPT][hapmap]
rs2092905	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs2108108	0.80[MKK][hapmap]
rs2236033	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[ASN][1000 genomes]
rs2281440	0.83[ASN][1000 genomes]
rs2295242	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2295251	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2387	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3804087	0.83[ASW][hapmap];0.83[MEX][hapmap]
rs3818134	0.95[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs4820051	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4820979	0.95[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs4820980	0.95[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs4820982	0.95[CEU][hapmap]
rs4820983	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap]
rs5749293	0.85[JPT][hapmap]
rs5749303	0.90[JPT][hapmap]
rs5749304	0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs5749306	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs5753667	0.95[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs5753681	0.85[JPT][hapmap]
rs5753686	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs5753691	0.84[JPT][hapmap]
rs5753713	0.84[ASN][1000 genomes]
rs5753714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs5753715	0.89[ASN][1000 genomes]
rs5753732	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5753733	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753734	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5994415	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs5994420	0.86[YRI][hapmap]
rs5998042	0.89[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs5998054	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs5998069	0.82[YRI][hapmap]
rs5998086	0.83[ASW][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap]
rs7287937	0.95[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7289075	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs738656	0.95[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs738684	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs738702	0.83[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs760908	0.83[ASW][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs761746	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs761747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8461	0.83[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9621279	0.82[EUR][1000 genomes]
rs9956	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7291918	SFI1	cis	cerebellum	SCAN

Chromatin state (count:120 , 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	chr22:31985800-32010400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr22:31985800-32012400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:31985800-32014400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr22:31985800-32014800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31990400-32014200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr22:31993200-32013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr22:31996000-32008400	Strong transcription	Primary T cells from cord blood	blood
16	chr22:31996200-32010000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr22:31996400-32010800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr22:31996600-32010600	Strong transcription	Thymus	Thymus
19	chr22:31996600-32011200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr22:31996600-32011800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr22:31996600-32012200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr22:31996600-32018200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr22:31996600-32020600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr22:31996800-32011600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr22:31997200-32012000	Strong transcription	Fetal Thymus	thymus
26	chr22:31997400-32010400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr22:31997600-32011400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr22:31998400-32015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:31998600-32022000	Weak transcription	Fetal Kidney	kidney
30	chr22:31998800-32010200	Weak transcription	Left Ventricle	heart
31	chr22:31998800-32012200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr22:31999000-32010000	Weak transcription	Right Ventricle	heart
33	chr22:31999000-32010200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:31999000-32010600	Weak transcription	Osteobl	bone
35	chr22:31999000-32011800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr22:31999000-32013800	Weak transcription	HMEC	breast
37	chr22:31999000-32014600	Weak transcription	NHDF-Ad	bronchial
38	chr22:31999200-32010600	Weak transcription	HUVEC	blood vessel
39	chr22:31999400-32008400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr22:31999400-32011400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr22:31999400-32011600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr22:31999400-32012800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:31999400-32014800	Weak transcription	NH-A	brain
44	chr22:31999600-32012200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr22:31999800-32012200	Weak transcription	Brain Substantia Nigra	brain
46	chr22:32000200-32014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr22:32001200-32012000	Weak transcription	Brain Hippocampus Middle	brain
48	chr22:32001600-32009800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr22:32001600-32011600	Weak transcription	Brain Germinal Matrix	brain
50	chr22:32001600-32012400	Weak transcription	NHEK	skin

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