Variant report

Variant	rs2446972
Chromosome Location	chr12:49256158-49256159
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49256150-49256221	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.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49211113..49212754-chr12:49254899..49256730,2	MCF-7	breast:
2	chr12:49244593..49247064-chr12:49254906..49256419,2	MCF-7	breast:

Variant related genes	Relation type
RND1	TF binding region
ENSG00000174243	Chromatin interaction
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1045340	0.82[JPT][hapmap]
rs1057908	0.83[JPT][hapmap]
rs10783285	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10875882	0.94[ASN][1000 genomes]
rs1565933	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs2453471	0.83[JPT][hapmap]
rs2453472	0.83[JPT][hapmap]
rs3759148	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3782360	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs4760597	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4760598	0.92[ASN][1000 genomes]
rs4760599	0.82[ASN][1000 genomes]
rs4760639	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2446972	RND1	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49246600-49258600	Weak transcription	Small Intestine	intestine
2	chr12:49246800-49256400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49247200-49256600	Weak transcription	Primary T cells from cord blood	blood
4	chr12:49247200-49257000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:49247200-49257800	Weak transcription	Stomach Mucosa	stomach
6	chr12:49247200-49258000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:49247200-49258600	Weak transcription	Esophagus	oesophagus
8	chr12:49247200-49258600	Weak transcription	Right Ventricle	heart
9	chr12:49247200-49258800	Weak transcription	Right Atrium	heart
10	chr12:49247200-49259000	Weak transcription	Ovary	ovary
11	chr12:49250000-49256200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:49251200-49256400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:49251200-49256600	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr12:49251200-49256600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:49251600-49257800	Weak transcription	Spleen	Spleen
16	chr12:49251800-49257400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:49252000-49257400	Weak transcription	GM12878-XiMat	blood
18	chr12:49252200-49256200	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:49252400-49257800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:49253400-49256200	Strong transcription	Fetal Stomach	stomach
21	chr12:49253600-49257000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:49253800-49258200	Weak transcription	HepG2	liver
23	chr12:49254400-49256400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:49254600-49256200	Enhancers	Fetal Brain Male	brain
25	chr12:49254600-49256600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:49254800-49257400	Genic enhancers	Liver	Liver
27	chr12:49254800-49259000	Transcr. at gene 5' and 3'	A549	lung
28	chr12:49255400-49256600	Strong transcription	Gastric	stomach
29	chr12:49255400-49256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:49255400-49257200	Weak transcription	Adipose Nuclei	Adipose
31	chr12:49255400-49257800	Weak transcription	Fetal Intestine Large	intestine
32	chr12:49255400-49258000	Weak transcription	Pancreas	Pancrea
33	chr12:49255600-49256200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:49255600-49256200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr12:49255600-49256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:49255600-49257800	Weak transcription	Fetal Intestine Small	intestine
37	chr12:49255800-49256200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:49255800-49256200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:49255800-49260200	Active TSS	Brain Angular Gyrus	brain
40	chr12:49256000-49256200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:49256000-49256200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:49256000-49256200	Active TSS	Brain Germinal Matrix	brain
43	chr12:49256000-49256400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:49256000-49256400	Weak transcription	Lung	lung
45	chr12:49256000-49256600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:49256000-49256600	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr12:49256000-49256800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:49256000-49257400	Weak transcription	Primary B cells from cord blood	blood
49	chr12:49256000-49258200	Flanking Active TSS	Fetal Brain Female	brain
50	chr12:49256000-49258400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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