Variant report

Variant	rs5753698
Chromosome Location	chr22:31970054-31970055
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:31961151-31976153..22:33253287-33262063	K562	blood:
2	chr22:31969040..31971908-chr22:31972285..31974264,2	MCF-7	breast:
3	22:31961151-31976153..22:32513817-32522138	K562	blood:
4	22:31961151-31976153..22:33030812-33041554	K562	blood:
5	22:31961151-31976153..22:32284948-32287956	K562	blood:

Variant related genes	Relation type
ENSG00000198089	Chromatin interaction
ENSG00000183531	Chromatin interaction
ENSG00000234479	Chromatin interaction
ENSG00000227813	Chromatin interaction
ENSG00000251890	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1018490	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs1968023	0.83[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap]
rs2273249	0.80[CEU][hapmap]
rs2273251	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs2899164	0.80[CEU][hapmap]
rs34538851	0.81[EUR][1000 genomes]
rs5749286	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs5749291	0.81[EUR][1000 genomes]
rs5749298	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs5753601	0.80[CEU][hapmap]
rs5753618	0.82[JPT][hapmap];0.85[MEX][hapmap]
rs5753632	0.80[CEU][hapmap]
rs5753639	0.80[CEU][hapmap]
rs5753659	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs5753669	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs5753671	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs5753723	0.83[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs5998042	0.82[JPT][hapmap]
rs5998058	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]
rs5998067	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes]
rs7284622	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs7285619	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs738657	0.80[CEU][hapmap]
rs8138525	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];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8142355	1.00[LWK][hapmap]
rs9606839	1.00[ASW][hapmap];0.80[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs9606843	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap]
rs9606848	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs9609296	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs9609297	1.00[CEU][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs9609304	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs9609329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv914979	chr22:31964043-31990184	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5753698	PISD	cis	cerebellum	SCAN
rs5753698	SFI1	cis	cerebellum	SCAN
rs5753698	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs5753698	SFI1	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31893400-31971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr22:31927400-31970200	Weak transcription	Fetal Lung	lung
3	chr22:31927400-31979400	Weak transcription	NHDF-Ad	bronchial
4	chr22:31927400-31980000	Weak transcription	HSMMtube	muscle
5	chr22:31927600-31974200	Weak transcription	Small Intestine	intestine
6	chr22:31929800-31985600	Weak transcription	Fetal Kidney	kidney
7	chr22:31933200-31971000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr22:31933600-31979600	Weak transcription	HUVEC	blood vessel
9	chr22:31934000-31981000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr22:31935200-31985400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:31935800-32013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr22:31941400-31981400	Weak transcription	NHEK	skin
13	chr22:31947000-31970200	Weak transcription	Brain Substantia Nigra	brain
14	chr22:31947000-31970200	Weak transcription	Fetal Muscle Leg	muscle
15	chr22:31947400-31970200	Weak transcription	Ovary	ovary
16	chr22:31947400-31971000	Weak transcription	Aorta	Aorta
17	chr22:31947400-31972800	Weak transcription	Esophagus	oesophagus
18	chr22:31947800-31970200	Weak transcription	Fetal Intestine Large	intestine
19	chr22:31947800-31970200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr22:31947800-31971000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr22:31947800-31971200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr22:31947800-32009600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr22:31948000-31973400	Weak transcription	Liver	Liver
24	chr22:31948200-31980000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr22:31949200-31971800	Weak transcription	NHLF	lung
26	chr22:31949200-31973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:31949200-31981600	Weak transcription	Left Ventricle	heart
28	chr22:31949400-32014400	Weak transcription	Hela-S3	cervix
29	chr22:31949600-31977800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr22:31949800-31976400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr22:31954400-31980000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr22:31955800-31971000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr22:31956200-31973400	Weak transcription	HSMM	muscle
34	chr22:31957200-31977800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr22:31957400-31974200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr22:31957400-32016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr22:31957600-31970200	Weak transcription	Brain Hippocampus Middle	brain
38	chr22:31957600-31970200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr22:31957600-31971200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr22:31957600-31973400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr22:31957800-31970200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr22:31957800-31970200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr22:31957800-31970400	Weak transcription	Brain Anterior Caudate	brain
44	chr22:31957800-31975800	Weak transcription	Stomach Mucosa	stomach
45	chr22:31957800-31975800	Weak transcription	A549	lung
46	chr22:31957800-31979600	Weak transcription	K562	blood
47	chr22:31958000-31971000	Weak transcription	GM12878-XiMat	blood
48	chr22:31958000-31975800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr22:31958000-31983000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr22:31958200-31970200	Weak transcription	Osteobl	bone

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