Variant report

Variant	rs17034938
Chromosome Location	chr12:104329212-104329213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr12:104328577-104332758	K562	blood:	n/a	chr12:104331442-104331450
2	POLR2A	chr12:104328944-104329280	K562	blood:	n/a	n/a
3	SPI1	chr12:104329152-104329433	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:104328780-104331091	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:104328593-104332706	K562	blood:	n/a	n/a
6	POLR2A	chr12:104328756-104331372	GM12891	blood:	n/a	n/a
7	TEAD4	chr12:104328661-104331517	K562	blood:	n/a	n/a
8	POLR2A	chr12:104328937-104331295	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:104328704-104331057	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:104328888-104330098	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:104328660-104333717	K562	blood:	n/a	n/a
12	POLR2A	chr12:104328937-104329237	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:104324071-104347835	K562	blood:	n/a	n/a
14	POLR2A	chr12:104328518-104331027	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:104328594-104331086	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:
2	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
3	chr12:104234323..104236282-chr12:104327727..104330455,2	K562	blood:
4	chr12:104233850..104236923-chr12:104328955..104330826,3	K562	blood:

No data

Variant related genes	Relation type
HSP90B1	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10745984	0.91[CEU][hapmap]
rs10778292	0.91[CEU][hapmap]
rs10861131	0.91[CEU][hapmap];0.84[MEX][hapmap]
rs10861142	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs10861143	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs10861146	0.91[CEU][hapmap]
rs11111815	0.91[CEU][hapmap]
rs12302488	0.81[CEU][hapmap]
rs12369947	0.81[CEU][hapmap]
rs12371102	0.90[CEU][hapmap]
rs3812801	0.83[CEU][hapmap];0.92[MEX][hapmap]
rs4135138	0.89[CHB][hapmap]
rs9308316	0.91[CEU][hapmap];1.00[MEX][hapmap]
rs9989004	0.90[CEU][hapmap]

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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17034938	HSP90B1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104325000-104331000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
2	chr12:104325200-104330000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:104325200-104330200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:104325600-104331000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:104325600-104348600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:104325600-104349800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104325800-104333400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:104325800-104335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104325800-104348600	Strong transcription	Placenta	Placenta
10	chr12:104326000-104331000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:104326000-104348800	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:104326200-104330200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:104326200-104330400	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr12:104326200-104331200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr12:104326400-104330800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:104326400-104331400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:104326400-104331400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:104326600-104329400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:104326600-104329600	Genic enhancers	Thymus	Thymus
20	chr12:104326600-104329800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:104326600-104330000	Genic enhancers	Primary T cells from cord blood	blood
22	chr12:104326600-104330000	Genic enhancers	Brain Cingulate Gyrus	brain
23	chr12:104326600-104330200	Genic enhancers	Adipose Nuclei	Adipose
24	chr12:104326600-104348800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:104326800-104330000	Genic enhancers	Brain Angular Gyrus	brain
26	chr12:104326800-104330400	Genic enhancers	Left Ventricle	heart
27	chr12:104326800-104344800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr12:104326800-104348800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:104326800-104348800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:104327000-104331200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:104327000-104341600	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:104327000-104348200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:104327000-104348600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:104327200-104329400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:104327200-104329400	Strong transcription	Brain Germinal Matrix	brain
36	chr12:104327200-104329600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:104327200-104329600	Genic enhancers	HUVEC	blood vessel
38	chr12:104327200-104330000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
39	chr12:104327200-104330200	Genic enhancers	Brain Anterior Caudate	brain
40	chr12:104327200-104330200	Genic enhancers	Fetal Thymus	thymus
41	chr12:104327200-104330800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:104327200-104330800	Genic enhancers	Liver	Liver
43	chr12:104327200-104331000	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:104327200-104331400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr12:104327200-104332200	Genic enhancers	HepG2	liver
46	chr12:104327200-104341800	Strong transcription	Fetal Kidney	kidney
47	chr12:104327200-104345000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:104327200-104345400	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr12:104327200-104348000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:104327200-104348200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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