Variant report

Variant	rs10878382
Chromosome Location	chr12:66523888-66523889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:66523828-66525082	GM18505	blood:	n/a	n/a
2	POLR2A	chr12:66523647-66524135	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:66523758-66525331	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:66523783-66525067	Raji	blood:	n/a	n/a
5	MTA3	chr12:66523668-66525489	GM12878	blood:	n/a	n/a
6	RFX5	chr12:66523773-66525271	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:66523869-66525164	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr12:66523781-66525012	GM12878	blood:	n/a	n/a
9	RCOR1	chr12:66523676-66525059	K562	blood:	n/a	n/a
10	POLR2A	chr12:66523654-66524916	GM12892	blood:	n/a	n/a
11	POLR2A	chr12:66523752-66525424	U87	brain:	n/a	n/a
12	POLR2A	chr12:66523776-66524086	HepG2	liver:	n/a	n/a
13	MXI1	chr12:66523620-66525402	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:66523641-66525025	GM12892	blood:	n/a	n/a
15	HEY1	chr12:66523737-66524924	K562	blood:	n/a	n/a
16	HCFC1	chr12:66523520-66525391	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:66523633-66524960	GM12878	blood:	n/a	n/a
18	PML	chr12:66523608-66525036	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:66523762-66524982	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:66523681-66524978	GM12891	blood:	n/a	n/a
21	SIN3AK20	chr12:66523680-66525159	MCF-7	breast:	n/a	n/a
22	POLR2A	chr12:66523620-66524988	GM12892	blood:	n/a	n/a
23	POLR2A	chr12:66523650-66526889	K562	blood:	n/a	n/a
24	ZMIZ1	chr12:66523882-66524951	K562	blood:	n/a	n/a
25	POLR2A	chr12:66523792-66525306	GM19099	blood:	n/a	n/a
26	MXI1	chr12:66523709-66525311	IMR90	lung:	n/a	n/a
27	POLR2A	chr12:66523820-66523931	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:66523863-66525346	K562	blood:	n/a	n/a
29	MAX	chr12:66523867-66525016	MCF-7	breast:	n/a	n/a
30	POLR2A	chr12:66523819-66524970	HL-60	blood:	n/a	n/a
31	POLR2A	chr12:66523762-66525405	HL-60	blood:	n/a	n/a
32	ELF1	chr12:66523867-66525201	HCT-116	colon:	n/a	chr12:66524534-66524547
33	POLR2A	chr12:66523664-66524871	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr12:66523777-66525163	HepG2	liver:	n/a	n/a
35	SIN3A	chr12:66523827-66524894	H1-hESC	embryonic stem cell:	n/a	chr12:66524632-66524641
36	GABPA	chr12:66523784-66525112	A549	lung:	n/a	n/a
37	POLR2A	chr12:66523764-66524977	Hela-S3	cervix:	n/a	n/a
38	TCF12	chr12:66523851-66525028	A549	lung:	n/a	n/a
39	POLR2A	chr12:66523771-66525017	HCT-116	colon:	n/a	n/a
40	POLR2A	chr12:66523618-66524842	IMR90	lung:	n/a	n/a
41	ELK1	chr12:66523868-66524068	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:66523705-66525567	GM12878	blood:	n/a	n/a
43	POLR2A	chr12:66523782-66525039	U87	brain:	n/a	n/a
44	POLR2A	chr12:66523792-66524960	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:66523757-66525063	PBDE	blood:	n/a	n/a
46	GABPA	chr12:66523584-66525368	MCF-7	breast:	n/a	n/a
47	POLR2A	chr12:66523552-66525187	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr12:66523872-66525146	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr12:66523787-66525179	K562	blood:	n/a	n/a
50	POLR2A	chr12:66523519-66525661	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:66523453..66525027-chr12:66562451..66564555,2	K562	blood:
2	chr12:66523792..66527078-chr12:66561013..66565049,6	MCF-7	breast:
3	chr1:145096186..145098889-chr12:66522673..66525529,2	MCF-7	breast:
4	chr12:66523081..66526604-chr12:66560988..66564576,8	MCF-7	breast:
5	chr12:66523095..66527368-chr12:66532414..66535159,4	MCF-7	breast:
6	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
7	chr12:66521057..66526734-chr12:66560807..66565257,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239335	TF binding region
ENSG00000155957	Chromatin interaction
ENSG00000127311	Chromatin interaction
ENSG00000223380	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10400539	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10506478	0.92[CEU][hapmap];0.91[CHD][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10735933	0.81[CHB][hapmap]
rs10878381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878383	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878389	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10878391	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176060	0.85[LWK][hapmap];0.86[MKK][hapmap]
rs11176063	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176065	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176067	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176068	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176080	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11176081	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11176082	0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12227630	0.85[EUR][1000 genomes]
rs12832926	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17767200	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882201	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1898304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1921083	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141709	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2178486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2870781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34645929	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34755483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4296075	0.80[AMR][1000 genomes]
rs4474482	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4575321	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56271210	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61927092	0.83[ASN][1000 genomes]
rs7295147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302893	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305938	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966453	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966561	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979775	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8793	0.85[LWK][hapmap];0.86[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10878382	TMBIM4	cis	uninvolved skin	skin_eQTL
rs10878382	RP11-745O10.2	cis	lung	GTEx
rs10878382	TMBIM4	cis	lesional skin	skin_eQTL
rs10878382	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878382	RP11-745O10.2	cis	Artery Tibial	GTEx
rs10878382	TMBIM4	cis	normal skin	skin_eQTL
rs10878382	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10878382	TMBIM4	cis	lymphoblastoid	seeQTL
rs10878382	RP11-745O10.2	cis	Thyroid	GTEx
rs10878382	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66516000-66524000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:66522600-66526000	Active TSS	GM12878-XiMat	blood
3	chr12:66523000-66524000	Flanking Active TSS	Dnd41	blood
4	chr12:66523000-66524200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:66523000-66525200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:66523000-66525800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:66523000-66526000	Active TSS	A549	lung
8	chr12:66523000-66526400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:66523200-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:66523200-66525400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:66523400-66524000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr12:66523400-66524000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr12:66523400-66524000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr12:66523400-66524000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:66523400-66524000	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr12:66523400-66524000	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr12:66523400-66524000	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr12:66523400-66524000	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr12:66523400-66524000	Flanking Active TSS	Fetal Brain Male	brain
20	chr12:66523400-66524000	Flanking Active TSS	Fetal Brain Female	brain
21	chr12:66523400-66524000	Flanking Active TSS	Fetal Heart	heart
22	chr12:66523400-66524000	Flanking Active TSS	Fetal Thymus	thymus
23	chr12:66523400-66524000	Flanking Active TSS	Osteobl	bone
24	chr12:66523400-66524200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:66523400-66524200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr12:66523400-66524200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr12:66523400-66524200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr12:66523400-66524200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr12:66523400-66524200	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr12:66523400-66524200	Flanking Active TSS	Liver	Liver
31	chr12:66523400-66524200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr12:66523400-66524400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr12:66523400-66525000	Active TSS	Fetal Lung	lung
34	chr12:66523400-66525200	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr12:66523400-66525200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr12:66523400-66525200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:66523400-66525200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:66523400-66525200	Active TSS	Fetal Intestine Small	intestine
39	chr12:66523400-66525200	Active TSS	NH-A	brain
40	chr12:66523400-66525200	Active TSS	NHDF-Ad	bronchial
41	chr12:66523400-66525400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:66523400-66525400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr12:66523400-66525400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:66523400-66525400	Active TSS	HSMMtube	muscle
45	chr12:66523400-66525400	Active TSS	NHLF	lung
46	chr12:66523400-66525600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:66523400-66525800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr12:66523600-66524000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr12:66523600-66524000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:66523600-66524000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links