Variant report

Variant	rs1457109
Chromosome Location	chr19:55935184-55935185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55926569..55928902-chr19:55933582..55936216,2	K562	blood:
2	chr19:55934305..55936521-chr19:55941153..55942887,2	K562	blood:
3	chr19:55934645..55937575-chr19:55940137..55944163,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10412033	0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs11668893	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1531215	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2384684	0.81[CEU][hapmap];0.87[CHD][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4075908	0.89[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4801603	0.82[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4801608	0.89[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6509941	0.82[ASN][1000 genomes]
rs72489180	0.85[EUR][1000 genomes]
rs7249831	0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs73606257	0.81[ASN][1000 genomes]
rs7507151	0.82[CEU][hapmap]
rs8107678	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
2	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
4	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
5	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1457109	SHISA7	cis	Nerve Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55931600-55937800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:55933000-55940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:55934800-55935200	Enhancers	Brain Angular Gyrus	brain
4	chr19:55934800-55935400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:55934800-55935400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:55934800-55935400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:55934800-55936800	Enhancers	Brain Hippocampus Middle	brain
8	chr19:55934800-55937000	Enhancers	Brain Anterior Caudate	brain
9	chr19:55935000-55935200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:55935000-55935200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr19:55935000-55935200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr19:55935000-55935200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:55935000-55935200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr19:55935000-55935200	Enhancers	Fetal Thymus	thymus
15	chr19:55935000-55935200	Enhancers	Thymus	Thymus
16	chr19:55935000-55935400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:55935000-55935400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr19:55935000-55935400	Bivalent Enhancer	K562	blood
19	chr19:55935000-55935400	Bivalent Enhancer	NHEK	skin
20	chr19:55935000-55935600	Enhancers	Brain Cingulate Gyrus	brain
21	chr19:55935000-55936800	Enhancers	Brain Substantia Nigra	brain

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