Variant report

Variant	rs1565933
Chromosome Location	chr12:49255798-49255799
allele	C/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:4)
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	chr12:49253272-49258971	A549	lung:	n/a	n/a
2	POLR2A	chr12:49255750-49255812	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:49255685-49255976	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49245571..49247224-chr12:49253107..49255933,2	K562	blood:
2	chr12:49211113..49212754-chr12:49254899..49256730,2	MCF-7	breast:
3	chr12:49253202..49256104-chr12:49256944..49260973,5	K562	blood:
4	chr12:49244593..49247064-chr12:49254906..49256419,2	MCF-7	breast:

No data

Variant related genes	Relation type
RND1	TF binding region
ENSG00000172602	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1045340	0.84[JPT][hapmap]
rs10783285	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]
rs10875882	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446972	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs3759148	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3782360	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760598	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760639	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1565933	FKBP11	cis	parietal	SCAN
rs1565933	RND1	cis	multi-tissue	Pritchard
rs1565933	ANO6	cis	parietal	SCAN
rs1565933	FKBP11	cis	cerebellum	SCAN
rs1565933	PLEKHA9	cis	parietal	SCAN

Chromatin state (count:55 , 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	chr12:49247200-49255800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:49247200-49255800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:49247200-49256000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:49247200-49256600	Weak transcription	Primary T cells from cord blood	blood
7	chr12:49247200-49257000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:49247200-49257800	Weak transcription	Stomach Mucosa	stomach
9	chr12:49247200-49258000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:49247200-49258600	Weak transcription	Esophagus	oesophagus
11	chr12:49247200-49258600	Weak transcription	Right Ventricle	heart
12	chr12:49247200-49258800	Weak transcription	Right Atrium	heart
13	chr12:49247200-49259000	Weak transcription	Ovary	ovary
14	chr12:49250000-49256200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:49251200-49256000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:49251200-49256000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:49251200-49256400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:49251200-49256600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr12:49251200-49256600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:49251600-49257800	Weak transcription	Spleen	Spleen
21	chr12:49251800-49257400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:49252000-49257400	Weak transcription	GM12878-XiMat	blood
23	chr12:49252200-49256200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:49252400-49257800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:49253400-49255800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:49253400-49256200	Strong transcription	Fetal Stomach	stomach
27	chr12:49253600-49257000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:49253800-49258200	Weak transcription	HepG2	liver
29	chr12:49254000-49255800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:49254400-49256000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:49254400-49256400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:49254600-49255800	Genic enhancers	Brain Angular Gyrus	brain
33	chr12:49254600-49256000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr12:49254600-49256000	Genic enhancers	Brain Anterior Caudate	brain
35	chr12:49254600-49256200	Enhancers	Fetal Brain Male	brain
36	chr12:49254600-49256600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:49254800-49255800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:49254800-49256000	Strong transcription	Primary B cells from cord blood	blood
39	chr12:49254800-49256000	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:49254800-49257400	Genic enhancers	Liver	Liver
41	chr12:49254800-49259000	Transcr. at gene 5' and 3'	A549	lung
42	chr12:49255000-49256000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
43	chr12:49255200-49256000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
44	chr12:49255200-49256000	Strong transcription	Lung	lung
45	chr12:49255400-49256600	Strong transcription	Gastric	stomach
46	chr12:49255400-49256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:49255400-49257200	Weak transcription	Adipose Nuclei	Adipose
48	chr12:49255400-49257800	Weak transcription	Fetal Intestine Large	intestine
49	chr12:49255400-49258000	Weak transcription	Pancreas	Pancrea
50	chr12:49255600-49255800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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