Variant report

Variant	rs785422
Chromosome Location	chr15:30173885-30173886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:30162335..30165638-chr15:30172933..30175702,3	K562	blood:
2	chr15:30171448..30173034-chr15:30173407..30175865,2	K562	blood:
3	chr15:30114093..30116162-chr15:30173109..30175872,2	K562	blood:

Variant related genes	Relation type
ENSG00000259523	Chromatin interaction
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1085231	0.97[EUR][1000 genomes]
rs2461738	0.87[EUR][1000 genomes]
rs62014488	0.86[EUR][1000 genomes]
rs62014489	0.90[EUR][1000 genomes]
rs62014490	0.90[EUR][1000 genomes]
rs711356	0.88[CEU][hapmap];1.00[EUR][1000 genomes]
rs711357	1.00[EUR][1000 genomes]
rs785420	0.97[EUR][1000 genomes]
rs785424	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs785429	0.97[EUR][1000 genomes]
rs785431	0.97[EUR][1000 genomes]
rs785432	0.95[EUR][1000 genomes]
rs785434	0.97[EUR][1000 genomes]
rs785435	0.97[EUR][1000 genomes]
rs785436	0.97[EUR][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	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv482572	chr15:30118905-30304529	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Corneal structure	23291589	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs785422	SNORD116-29	cis	parietal	SCAN
rs785422	SNORD115-41	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30164400-30174600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:30165200-30175000	Weak transcription	Right Atrium	heart
3	chr15:30165400-30174800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:30165400-30175400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:30167600-30174400	Weak transcription	Fetal Kidney	kidney
6	chr15:30170600-30174800	Weak transcription	Fetal Muscle Leg	muscle
7	chr15:30170600-30178000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr15:30170600-30178200	Enhancers	Brain Hippocampus Middle	brain
9	chr15:30170800-30177400	Enhancers	Brain Substantia Nigra	brain
10	chr15:30170800-30178400	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:30171000-30174800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:30171000-30181000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:30171400-30177400	Enhancers	Brain Anterior Caudate	brain
14	chr15:30172400-30178600	Enhancers	Brain Angular Gyrus	brain
15	chr15:30172800-30174000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:30173000-30174800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:30173200-30174800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:30173800-30174800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:30173800-30175200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:30173800-30175200	Weak transcription	HSMMtube	muscle

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