Variant report

Variant	rs10783285
Chromosome Location	chr12:49257328-49257329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49257228-49257418	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:49255873-49258188	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:49253272-49258971	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49253202..49256104-chr12:49256944..49260973,5	K562	blood:
2	chr12:49250166..49253023-chr12:49256244..49259199,2	K562	blood:
3	chr12:49244737..49248613-chr12:49256890..49261439,8	MCF-7	breast:
4	chr12:49257214..49258853-chr12:49292105..49293671,2	MCF-7	breast:
5	chr12:49256218..49258210-chr12:49380440..49382850,2	MCF-7	breast:

No data

Variant related genes	Relation type
RND1	TF binding region
ENSG00000172602	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1045340	0.89[JPT][hapmap]
rs10875882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565933	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446972	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs3759148	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs3782360	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760598	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760599	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760639	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10783285	RND1	cis	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49246600-49258600	Weak transcription	Small Intestine	intestine
2	chr12:49247200-49257800	Weak transcription	Stomach Mucosa	stomach
3	chr12:49247200-49258000	Weak transcription	Brain Substantia Nigra	brain
4	chr12:49247200-49258600	Weak transcription	Esophagus	oesophagus
5	chr12:49247200-49258600	Weak transcription	Right Ventricle	heart
6	chr12:49247200-49258800	Weak transcription	Right Atrium	heart
7	chr12:49247200-49259000	Weak transcription	Ovary	ovary
8	chr12:49251600-49257800	Weak transcription	Spleen	Spleen
9	chr12:49251800-49257400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:49252000-49257400	Weak transcription	GM12878-XiMat	blood
11	chr12:49252400-49257800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:49253800-49258200	Weak transcription	HepG2	liver
13	chr12:49254800-49257400	Genic enhancers	Liver	Liver
14	chr12:49254800-49259000	Transcr. at gene 5' and 3'	A549	lung
15	chr12:49255400-49257800	Weak transcription	Fetal Intestine Large	intestine
16	chr12:49255400-49258000	Weak transcription	Pancreas	Pancrea
17	chr12:49255600-49257800	Weak transcription	Fetal Intestine Small	intestine
18	chr12:49255800-49260200	Active TSS	Brain Angular Gyrus	brain
19	chr12:49256000-49257400	Weak transcription	Primary B cells from cord blood	blood
20	chr12:49256000-49258200	Flanking Active TSS	Fetal Brain Female	brain
21	chr12:49256000-49258400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:49256000-49258400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:49256000-49260200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:49256200-49257400	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr12:49256200-49257800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:49256200-49257800	Active TSS	Brain Hippocampus Middle	brain
27	chr12:49256200-49259000	Flanking Active TSS	Fetal Brain Male	brain
28	chr12:49256200-49259400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:49256200-49259800	Active TSS	Brain Cingulate Gyrus	brain
30	chr12:49256400-49257400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr12:49256400-49257600	Enhancers	Fetal Kidney	kidney
32	chr12:49256400-49258000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr12:49256400-49258000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:49256400-49258400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:49256400-49258800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:49256400-49260200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr12:49256600-49257400	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr12:49256600-49257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:49256600-49260000	Active TSS	Brain Anterior Caudate	brain
40	chr12:49256800-49257800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:49256800-49258000	Enhancers	Gastric	stomach
42	chr12:49256800-49258400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr12:49257000-49257600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
44	chr12:49257000-49257600	Weak transcription	Lung	lung
45	chr12:49257000-49257800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr12:49257000-49258400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr12:49257200-49257400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr12:49257200-49257400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:49257200-49257400	Bivalent Enhancer	K562	blood
50	chr12:49257200-49258200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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