Variant report

Variant	rs17034946
Chromosome Location	chr12:104331157-104331158
allele	C/T
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	MXI1	chr12:104331145-104331511	K562	blood:	n/a	n/a
2	POLR2A	chr12:104329405-104331548	HepG2	liver:	n/a	n/a
3	PML	chr12:104328577-104332758	K562	blood:	n/a	chr12:104331442-104331450
4	POLR2A	chr12:104331144-104331375	K562	blood:	n/a	n/a
5	POLR2A	chr12:104328593-104332706	K562	blood:	n/a	n/a
6	BCLAF1	chr12:104329940-104331216	K562	blood:	n/a	n/a
7	POLR2A	chr12:104330990-104331166	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:104328756-104331372	GM12891	blood:	n/a	n/a
9	TEAD4	chr12:104328661-104331517	K562	blood:	n/a	n/a
10	POLR2A	chr12:104328937-104331295	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:104328660-104333717	K562	blood:	n/a	n/a
12	POLR2A	chr12:104324071-104347835	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:
2	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:

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

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10778307	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11111864	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11553765	0.81[AMR][1000 genomes]
rs12426161	1.00[AFR][1000 genomes]
rs12426382	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427041	1.00[AFR][1000 genomes]
rs12582800	1.00[AFR][1000 genomes]
rs17034880	1.00[AFR][1000 genomes]
rs17034911	1.00[AFR][1000 genomes]
rs17034914	1.00[AFR][1000 genomes]
rs17034960	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035056	0.84[ASN][1000 genomes]
rs17035129	0.81[AMR][1000 genomes]
rs17795947	1.00[AFR][1000 genomes]
rs1882019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293619	0.85[ASN][1000 genomes]
rs2293626	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2629805	0.87[ASN][1000 genomes]
rs2722200	0.94[ASN][1000 genomes]
rs2888805	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751207	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3751208	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3829300	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135060	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135065	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4135076	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135078	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135082	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135085	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135086	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135087	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135094	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4135095	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135118	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135131	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4135150	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55780086	0.94[EUR][1000 genomes]
rs55871448	0.81[AMR][1000 genomes]
rs55893407	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55919036	1.00[AFR][1000 genomes]
rs56040534	1.00[AFR][1000 genomes]
rs60534873	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6615	1.00[AFR][1000 genomes]
rs728167	1.00[AFR][1000 genomes]
rs9788014	1.00[AFR][1000 genomes]
rs9788136	1.00[AFR][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104325600-104348600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:104325600-104349800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:104325800-104333400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:104325800-104335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:104325800-104348600	Strong transcription	Placenta	Placenta
6	chr12:104326000-104348800	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:104326200-104331200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr12:104326400-104331400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr12:104326400-104331400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr12:104326600-104348800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr12:104326800-104344800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr12:104326800-104348800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:104326800-104348800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:104327000-104331200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:104327000-104341600	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:104327000-104348200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:104327000-104348600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:104327200-104331400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr12:104327200-104332200	Genic enhancers	HepG2	liver
20	chr12:104327200-104341800	Strong transcription	Fetal Kidney	kidney
21	chr12:104327200-104345000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:104327200-104345400	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr12:104327200-104348000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:104327200-104348200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:104327200-104348400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:104327200-104348600	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:104327200-104348600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:104327200-104348600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:104327200-104348600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:104327200-104348600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:104327200-104348800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:104327200-104348800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:104327200-104349000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:104327200-104349200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:104327400-104340000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:104327400-104348000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr12:104327400-104348000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:104327400-104348200	Strong transcription	HSMM	muscle
39	chr12:104327600-104332600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:104327600-104333200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:104327800-104333200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:104327800-104348400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:104327800-104348400	Strong transcription	Primary B cells from cord blood	blood
44	chr12:104328000-104333400	Strong transcription	HSMMtube	muscle
45	chr12:104328000-104340600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:104328000-104341800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:104328200-104344800	Strong transcription	Brain Substantia Nigra	brain
48	chr12:104328200-104348600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:104328200-104348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:104328400-104333400	Strong transcription	Fetal Stomach	stomach

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