Variant report

Variant	rs1397308
Chromosome Location	chr8:90640722-90640723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:90639321..90642147-chr8:90642418..90643951,2	K562	blood:
2	chr8:90633001..90635193-chr8:90639788..90641553,2	MCF-7	breast:
3	chr8:90638748..90641688-chr8:90643639..90646193,2	K562	blood:

Variant related genes	Relation type
ENSG00000251136	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1003843	0.81[CEU][hapmap]
rs10102245	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10112852	0.81[CEU][hapmap]
rs12545569	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12675281	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1605996	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1605997	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs218895	0.81[AFR][1000 genomes]
rs218899	0.84[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs218900	0.84[CEU][hapmap]
rs218901	0.84[CEU][hapmap]
rs218902	0.84[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs218903	0.84[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs218907	0.81[CEU][hapmap]
rs218908	0.81[CEU][hapmap]
rs218913	0.81[CEU][hapmap]
rs218916	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs218929	0.81[CEU][hapmap]
rs218944	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs218947	0.85[AFR][1000 genomes]
rs39499	0.81[CEU][hapmap]
rs39500	0.81[CEU][hapmap]
rs39506	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs39761	0.81[CEU][hapmap]
rs402886	0.81[CEU][hapmap]
rs40452	0.81[CEU][hapmap]
rs40453	0.84[MEX][hapmap]
rs42490	0.81[CEU][hapmap]
rs43134	0.81[CEU][hapmap]
rs43225	0.81[CEU][hapmap]
rs447618	0.80[CEU][hapmap];0.83[MEX][hapmap]
rs4961154	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4961155	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4961158	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56291556	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7824932	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465735	chr8:89760311-90729507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv611714	chr8:89760311-90729507	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1028969	chr8:90475194-90650295	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv427825	chr8:90495139-90653696	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv870380	chr8:90546585-90720182	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1028026	chr8:90553930-90678631	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv982109	chr8:90556188-90703631	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1026523	chr8:90558935-90722580	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv831389	chr8:90575517-90753120	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv1017263	chr8:90605445-90722580	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1397308	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs1397308	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs1397308	TMEM64	cis	parietal	SCAN
rs1397308	RIPK2	cis	cerebellum	SCAN
rs1397308	RIPK2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90599600-90650800	Weak transcription	Left Ventricle	heart
2	chr8:90616000-90652600	Weak transcription	Ovary	ovary
3	chr8:90624600-90642800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:90626000-90649200	Weak transcription	Brain Angular Gyrus	brain
5	chr8:90629400-90644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:90629400-90659000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr8:90631200-90642000	Weak transcription	HSMMtube	muscle
8	chr8:90635200-90641600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr8:90636600-90642600	Weak transcription	Lung	lung
10	chr8:90636800-90642000	Weak transcription	Gastric	stomach
11	chr8:90637400-90641200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:90637600-90643000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr8:90640400-90640800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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