Variant report

Variant	rs10778306
Chromosome Location	chr12:104325725-104325726
allele	A/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	TEAD4	chr12:104322407-104327510	K562	blood:	n/a	n/a
2	POLR2A	chr12:104323006-104326144	IMR90	lung:	n/a	n/a
3	RFX5	chr12:104322611-104325806	SK-N-SH	brain:	n/a	chr12:104323780-104323789 chr12:104323777-104323791 chr12:104323779-104323794 chr12:104323779-104323794 chr12:104323779-104323794 chr12:104323778-104323795
4	POLR2A	chr12:104323989-104328526	K562	blood:	n/a	n/a
5	POLR2A	chr12:104322439-104326717	MCF10A-Er-Src	breast:	n/a	n/a
6	PML	chr12:104323762-104328552	K562	blood:	n/a	n/a
7	POLR2A	chr12:104323674-104325727	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr12:104321755-104325879	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr12:104323206-104325740	K562	blood:	n/a	n/a
10	POLR2A	chr12:104325613-104326105	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:104320257-104326275	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr12:104325255-104325901	K562	blood:	n/a	n/a
13	POLR2A	chr12:104321807-104325757	GM12892	blood:	n/a	n/a
14	POLR2A	chr12:104321980-104325932	GM19099	blood:	n/a	n/a
15	POLR2A	chr12:104322047-104327304	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:104322411-104328493	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:104325358-104325780	HCT-116	colon:	n/a	n/a
18	POLR2A	chr12:104321935-104326151	GM12891	blood:	n/a	n/a
19	E2F4	chr12:104325501-104325977	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr12:104325610-104325767	MCF10A-Er-Src	breast:	n/a	n/a
21	MXI1	chr12:104325676-104326180	K562	blood:	n/a	n/a
22	POLR2A	chr12:104323743-104328568	K562	blood:	n/a	n/a
23	POLR2A	chr12:104321950-104327416	GM12878	blood:	n/a	n/a
24	CHD1	chr12:104325652-104325988	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:104324071-104347835	K562	blood:	n/a	n/a
26	BCLAF1	chr12:104323989-104326725	K562	blood:	n/a	chr12:104324626-104324634 chr12:104324880-104324889
27	POLR2A	chr12:104322522-104327427	MCF10A-Er-Src	breast:	n/a	n/a
28	MYC	chr12:104325661-104325861	MCF10A-Er-Src	breast:	n/a	n/a
29	MXI1	chr12:104322029-104326653	IMR90	lung:	n/a	chr12:104323780-104323795 chr12:104323778-104323793
30	POLR2A	chr12:104324658-104325739	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104320418..104331406-chr12:104346801..104355501,25	MCF-7	breast:
2	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
3	chr12:104319631..104321504-chr12:104324248..104326474,2	MCF-7	breast:
4	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
5	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
6	chr1:46152208..46153875-chr12:104323647..104326577,2	K562	blood:
7	chr12:104276555..104279337-chr12:104325468..104328815,4	K562	blood:
8	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000204954	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10861142	0.86[MKK][hapmap];0.87[YRI][hapmap]
rs10861143	0.86[MKK][hapmap];0.87[YRI][hapmap]
rs10861150	0.82[YRI][hapmap]
rs11111845	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11612613	0.88[JPT][hapmap]
rs12427041	0.84[ASN][1000 genomes]
rs12582800	0.87[JPT][hapmap]
rs12582917	0.82[JPT][hapmap]
rs17034880	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs17034911	0.83[ASN][1000 genomes]
rs17034914	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs17795947	0.88[JPT][hapmap]
rs2033729	0.90[AFR][1000 genomes]
rs2576942	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2722189	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs56040534	0.82[ASN][1000 genomes]
rs6615	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs728167	0.88[JPT][hapmap]
rs7306515	0.82[YRI][hapmap]
rs9308316	0.89[MKK][hapmap];0.87[YRI][hapmap]
rs9788014	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9788136	0.88[JPT][hapmap];0.82[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10778306	ACTR6	cis	cerebellum	SCAN
rs10778306	NFYB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104322200-104326200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr12:104322200-104326200	Active TSS	GM12878-XiMat	blood
3	chr12:104322400-104325800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:104322400-104326000	Active TSS	Colonic Mucosa	Colon
5	chr12:104322400-104326000	Active TSS	Fetal Intestine Small	intestine
6	chr12:104322400-104327000	Active TSS	Right Atrium	heart
7	chr12:104322600-104325800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:104322600-104325800	Active TSS	Fetal Muscle Trunk	muscle
9	chr12:104322600-104326400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:104322600-104327000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:104322600-104327200	Active TSS	Aorta	Aorta
12	chr12:104322800-104326000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:104322800-104326000	Active TSS	Fetal Intestine Large	intestine
14	chr12:104322800-104326000	Active TSS	NHDF-Ad	bronchial
15	chr12:104322800-104326200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:104322800-104326200	Active TSS	Fetal Stomach	stomach
17	chr12:104322800-104326200	Active TSS	Ovary	ovary
18	chr12:104322800-104326600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:104322800-104326800	Active TSS	Right Ventricle	heart
20	chr12:104323000-104325800	Active TSS	Colon Smooth Muscle	Colon
21	chr12:104323000-104326000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:104323000-104326000	Active TSS	Fetal Muscle Leg	muscle
23	chr12:104323000-104326200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:104323000-104326200	Active TSS	Psoas Muscle	Psoas
25	chr12:104323200-104325800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:104323200-104326400	Active TSS	HSMMtube	muscle
27	chr12:104323600-104325800	Active TSS	Fetal Thymus	thymus
28	chr12:104324200-104325800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr12:104324200-104325800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:104324600-104325800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr12:104324600-104326000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr12:104324600-104326200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:104324600-104326200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr12:104324600-104326200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr12:104324600-104327200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:104324800-104325800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:104324800-104326000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr12:104324800-104326200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr12:104324800-104327400	Transcr. at gene 5' and 3'	Dnd41	blood
40	chr12:104325000-104326000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr12:104325000-104326000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:104325000-104326200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:104325000-104326600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
44	chr12:104325000-104326600	Transcr. at gene 5' and 3'	Fetal Lung	lung
45	chr12:104325000-104326800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
46	chr12:104325000-104327400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:104325000-104327400	Transcr. at gene 5' and 3'	A549	lung
48	chr12:104325000-104327400	Transcr. at gene 5' and 3'	K562	blood
49	chr12:104325000-104329200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:104325000-104331000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast

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