Variant report

Variant	rs12296387
Chromosome Location	chr12:56523354-56523355
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	POLR2A	chr12:56522868-56523789	GM12892	blood:	n/a	n/a
2	SIN3A	chr12:56522347-56523412	GM12878	blood:	n/a	n/a
3	ZMIZ1	chr12:56522765-56523403	K562	blood:	n/a	n/a
4	HEY1	chr12:56521897-56523420	K562	blood:	n/a	chr12:56523052-56523067
5	JUND	chr12:56520974-56523643	SK-N-SH	brain:	n/a	chr12:56522465-56522476 chr12:56523527-56523539 chr12:56521688-56521697
6	EBF1	chr12:56522903-56523388	GM12878	blood:	n/a	n/a
7	MAX	chr12:56522791-56523386	K562	blood:	n/a	n/a
8	EGR1	chr12:56522715-56523498	MCF-7	breast:	n/a	chr12:56523124-56523146 chr12:56523129-56523142 chr12:56523128-56523143 chr12:56523130-56523140 chr12:56523090-56523104 chr12:56523128-56523142 chr12:56523130-56523141 chr12:56523126-56523140
9	MAZ	chr12:56521172-56523871	IMR90	lung:	n/a	chr12:56521713-56521728 chr12:56521717-56521726 chr12:56522529-56522539
10	SIN3AK20	chr12:56521221-56523702	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:56521501-56523764	K562	blood:	n/a	n/a
12	MXI1	chr12:56521241-56523795	SK-N-SH	brain:	n/a	chr12:56521716-56521725
13	MAZ	chr12:56522682-56523469	K562	blood:	n/a	n/a
14	POLR2A	chr12:56522546-56523439	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:56520805-56523448	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr12:56522854-56523491	GM18505	blood:	n/a	n/a
17	REST	chr12:56522960-56523451	SK-N-SH	brain:	n/a	chr12:56523112-56523130
18	PML	chr12:56522705-56523584	GM12878	blood:	n/a	chr12:56523246-56523254
19	TEAD4	chr12:56522611-56523681	K562	blood:	n/a	n/a
20	POLR2A	chr12:56522912-56523512	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:56522794-56523363	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:56522613-56523474	HUVEC	blood vessel:	n/a	n/a
23	MAX	chr12:56522883-56523391	SK-N-SH	brain:	n/a	n/a
24	PML	chr12:56522443-56523380	K562	blood:	n/a	chr12:56523246-56523254
25	MAX	chr12:56521508-56523415	NB4	blood:	n/a	chr12:56521713-56521728 chr12:56521717-56521726 chr12:56522529-56522539
26	JUND	chr12:56521087-56523745	GM12878	blood:	n/a	chr12:56522465-56522476 chr12:56523527-56523539 chr12:56521688-56521697
27	POLR2A	chr12:56521513-56523369	ECC-1	luminal epithelium:	n/a	n/a
28	YY1	chr12:56522899-56523400	K562	blood:	n/a	n/a
29	EGR1	chr12:56522542-56523624	HCT-116	colon:	n/a	chr12:56523124-56523146 chr12:56523129-56523142 chr12:56523128-56523143 chr12:56523130-56523140 chr12:56523090-56523104 chr12:56523128-56523142 chr12:56523130-56523141 chr12:56523126-56523140
30	RUNX3	chr12:56522751-56523780	GM12878	blood:	n/a	n/a
31	REST	chr12:56521259-56523411	H1-neurons	neurons:	n/a	chr12:56523112-56523130 chr12:56522578-56522588
32	MAX	chr12:56521271-56523367	ECC-1	luminal epithelium:	n/a	chr12:56521713-56521728 chr12:56521717-56521726 chr12:56522529-56522539
33	NR2F2	chr12:56522652-56523579	K562	blood:	n/a	n/a
34	ZBTB7A	chr12:56522679-56523477	ECC-1	luminal epithelium:	n/a	n/a
35	UBTF	chr12:56519897-56523387	K562	blood:	n/a	n/a
36	POLR2A	chr12:56522798-56523487	H1-neurons	neurons:	n/a	n/a
37	STAT5A	chr12:56521466-56523410	GM12878	blood:	n/a	chr12:56521490-56521498
38	POLR2A	chr12:56521240-56523586	H1-hESC	embryonic stem cell:	n/a	n/a
39	EBF1	chr12:56523089-56523383	GM12878	blood:	n/a	n/a
40	TFAP2C	chr12:56521680-56523418	Hela-S3	cervix:	n/a	chr12:56522023-56522038
41	POLR2A	chr12:56522843-56523451	GM12892	blood:	n/a	n/a
42	BHLHE40	chr12:56521378-56523613	K562	blood:	n/a	chr12:56523056-56523072
43	POLR2A	chr12:56522898-56523401	GM10847	blood:	n/a	n/a
44	KAP1	chr12:56523077-56523524	U2OS	brain:	n/a	chr12:56523246-56523254
45	JUN	chr12:56523034-56523538	K562	blood:	n/a	n/a
46	JUN	chr12:56519767-56523853	K562	blood:	n/a	chr12:56523527-56523539 chr12:56521688-56521697 chr12:56520630-56520639 chr12:56520216-56520227 chr12:56521687-56521700
47	REST	chr12:56522869-56523381	PFSK-1	brain:	n/a	chr12:56523112-56523130
48	POLR2A	chr12:56522926-56523399	GM12878	blood:	n/a	n/a
49	POLR2A	chr12:56522871-56523641	GM12878	blood:	n/a	n/a
50	IRF1	chr12:56522983-56523394	K562	blood:	n/a	chr12:56523339-56523351

No.	Distal block	Cell Line	Cell type
1	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:
2	chr12:56507991..56525761-chr12:56579808..56586137,68	MCF-7	breast:
3	chr12:56433873..56442113-chr12:56515349..56524351,14	K562	blood:
4	chr12:56518236..56525779-chr12:56581707..56584752,14	MCF-7	breast:
5	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
6	chr12:56522742..56523657-chrX:16737074..16738046,2	NB4	blood:
7	chr12:56521570..56523702-chr12:56622479..56624701,2	MCF-7	breast:
8	chr11:62608615..62609527-chr12:56522704..56523607,2	Hela-S3	cervix:
9	chr12:56434287..56437375-chr12:56519229..56523765,7	K562	blood:
10	chr12:56520558..56523356-chr12:56614094..56616710,4	K562	blood:
11	chr12:56519569..56524417-chr12:56555136..56559386,7	MCF-7	breast:
12	chr12:56521888..56524004-chr12:56719736..56721397,2	K562	blood:
13	chr12:56519631..56523356-chr12:56615060..56618173,5	K562	blood:
14	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258317	TF binding region
ESYT1	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000135473	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000169895	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000139540	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10129008	0.87[AFR][1000 genomes]
rs10747761	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11171746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11171753	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs11171754	0.97[AFR][1000 genomes]
rs11171755	0.97[AFR][1000 genomes]
rs11504023	0.80[AFR][1000 genomes]
rs12227040	1.00[GIH][hapmap]
rs12298136	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309480	0.82[AFR][1000 genomes]
rs12309692	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118317	1.00[JPT][hapmap]
rs17118378	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs28546848	0.90[AFR][1000 genomes]
rs28676339	0.97[AFR][1000 genomes]
rs4759226	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7975486	1.00[MEX][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56520000-56523800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr12:56520000-56524200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr12:56521000-56523400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:56521000-56523600	Active TSS	Aorta	Aorta
5	chr12:56521000-56523800	Active TSS	Right Atrium	heart
6	chr12:56521200-56523400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr12:56521200-56523400	Active TSS	Fetal Kidney	kidney
8	chr12:56521200-56523600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:56521200-56523800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:56521200-56524000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56521200-56524000	Active TSS	NHDF-Ad	bronchial
12	chr12:56521400-56523400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:56521400-56523400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:56521400-56523400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:56521400-56523400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr12:56521400-56523400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:56521400-56523400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:56521400-56523400	Active TSS	Brain Angular Gyrus	brain
19	chr12:56521400-56523400	Active TSS	Colon Smooth Muscle	Colon
20	chr12:56521400-56523400	Active TSS	Osteobl	bone
21	chr12:56521400-56523600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr12:56521400-56523600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:56521400-56523600	Active TSS	Left Ventricle	heart
24	chr12:56521400-56523600	Active TSS	Ovary	ovary
25	chr12:56521400-56523600	Active TSS	Psoas Muscle	Psoas
26	chr12:56521400-56523800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:56521400-56523800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:56521600-56523400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:56521600-56523400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:56521600-56523400	Active TSS	Primary T cells from cord blood	blood
31	chr12:56521600-56523400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:56521600-56523400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr12:56521600-56523400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr12:56521600-56523400	Active TSS	Brain Cingulate Gyrus	brain
35	chr12:56521600-56523400	Active TSS	Fetal Lung	lung
36	chr12:56521600-56523400	Active TSS	Hela-S3	cervix
37	chr12:56521600-56523400	Active TSS	HMEC	breast
38	chr12:56521600-56523600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:56521600-56523600	Active TSS	Lung	lung
40	chr12:56521600-56523800	Active TSS	Brain Substantia Nigra	brain
41	chr12:56521600-56523800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr12:56521600-56523800	Active TSS	GM12878-XiMat	blood
43	chr12:56521600-56523800	Active TSS	NHLF	lung
44	chr12:56521600-56524000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr12:56521600-56524200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:56521600-56524200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:56521800-56523400	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr12:56521800-56523600	Active TSS	Thymus	Thymus
49	chr12:56521800-56524000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:56522000-56523400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links