Variant report

Variant	rs7138930
Chromosome Location	chr12:49108488-49108489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49072667..49077768-chr12:49107571..49112359,8	MCF-7	breast:
2	chr12:49108385..49110371-chr12:49210566..49212165,2	MCF-7	breast:
3	chr12:49103301..49108658-chr12:49108679..49112078,7	K562	blood:
4	chr12:49073439..49079132-chr12:49108039..49112179,15	K562	blood:
5	chr12:49106870..49108564-chr12:49207751..49210118,2	MCF-7	breast:
6	chr12:49072639..49079132-chr12:49108469..49112073,12	K562	blood:
7	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167535	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000129315	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10783277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783278	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs10875849	0.83[CEU][hapmap]
rs10875861	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs12426435	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs2277366	0.88[CEU][hapmap]
rs3209584	0.84[CEU][hapmap]
rs3741628	0.84[CEU][hapmap]
rs3741629	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs3741630	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs3741632	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs3803025	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs3943899	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs4760740	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs6580689	0.84[CEU][hapmap]
rs6580692	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580693	0.81[EUR][1000 genomes]
rs7133756	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs7139119	0.81[EUR][1000 genomes]
rs7139236	0.84[CEU][hapmap]
rs7305907	0.81[EUR][1000 genomes]
rs7314665	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs7954446	0.81[EUR][1000 genomes]
rs7954548	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs7964546	0.81[EUR][1000 genomes]
rs7964848	0.81[EUR][1000 genomes]
rs7974625	0.80[EUR][1000 genomes]
rs7975030	0.88[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9634241	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs9634262	0.88[CEU][hapmap];0.86[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7138930	ZNF641	cis	cerebellum	SCAN
rs7138930	SNORA2B	cis	cerebellum	SCAN
rs7138930	ADCY6	cis	parietal	SCAN
rs7138930	C12orf54	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:49082200-49108600	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:49082200-49108600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:49082200-49108800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:49095000-49108600	Strong transcription	Fetal Stomach	stomach
7	chr12:49095600-49108800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:49097600-49108600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:49097600-49109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:49098200-49109600	Weak transcription	Aorta	Aorta
11	chr12:49098800-49108600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:49099200-49108600	Weak transcription	Gastric	stomach
13	chr12:49099200-49108800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:49099600-49109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:49099800-49108600	Weak transcription	Esophagus	oesophagus
16	chr12:49101000-49109000	Weak transcription	HSMMtube	muscle
17	chr12:49103000-49108600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:49103600-49108600	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr12:49104200-49108600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:49104600-49108600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:49105400-49109400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:49106000-49108600	Strong transcription	HSMM	muscle
23	chr12:49106400-49109000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:49106400-49109400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:49106600-49109000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:49107000-49108600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:49107000-49109000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr12:49107200-49108600	Genic enhancers	Adipose Nuclei	Adipose
29	chr12:49107200-49108600	Genic enhancers	Brain Germinal Matrix	brain
30	chr12:49107200-49108600	Strong transcription	NHDF-Ad	bronchial
31	chr12:49107200-49108800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:49107200-49109000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:49107200-49109200	Transcr. at gene 5' and 3'	Hela-S3	cervix
34	chr12:49107200-49109800	Enhancers	Small Intestine	intestine
35	chr12:49107200-49110400	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr12:49107400-49108600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:49107400-49108600	Genic enhancers	Primary T cells from cord blood	blood
38	chr12:49107400-49108600	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr12:49107400-49108800	Genic enhancers	Placenta	Placenta
40	chr12:49107400-49108800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr12:49107400-49109000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:49107400-49109000	Genic enhancers	Left Ventricle	heart
43	chr12:49107400-49109000	Flanking Active TSS	HepG2	liver
44	chr12:49107600-49108600	Genic enhancers	HUVEC	blood vessel
45	chr12:49107600-49108800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:49107600-49109000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
47	chr12:49107600-49109200	Transcr. at gene 5' and 3'	A549	lung
48	chr12:49107600-49109400	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr12:49107600-49109400	Genic enhancers	Fetal Thymus	thymus
50	chr12:49107600-49109600	Enhancers	Brain Angular Gyrus	brain

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