Variant report

Variant	rs55913294
Chromosome Location	chr12:48223554-48223555
allele	C/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	TCF12	chr12:48222548-48223731	ECC-1	luminal epithelium:	n/a	n/a
2	IRF1	chr12:48222726-48223607	K562	blood:	n/a	n/a
3	HCFC1	chr12:48221878-48223769	Hela-S3	cervix:	n/a	n/a
4	MYC	chr12:48222736-48223681	K562	blood:	n/a	chr12:48222924-48222934
5	EGR1	chr12:48222708-48223735	ECC-1	luminal epithelium:	n/a	chr12:48223198-48223213 chr12:48223201-48223211 chr12:48223200-48223211 chr12:48223201-48223211 chr12:48223199-48223212 chr12:48223200-48223211 chr12:48223199-48223212 chr12:48223199-48223213 chr12:48223195-48223217
6	EP300	chr12:48222692-48223686	K562	blood:	n/a	n/a
7	UBTF	chr12:48222715-48223602	K562	blood:	n/a	n/a
8	TEAD4	chr12:48222699-48223787	K562	blood:	n/a	n/a
9	POLR2A	chr12:48222491-48223691	K562	blood:	n/a	n/a
10	POLR2A	chr12:48222007-48223728	Hela-S3	cervix:	n/a	n/a
11	SMARCC1	chr12:48222049-48223592	Hela-S3	cervix:	n/a	n/a
12	JUN	chr12:48222338-48223775	K562	blood:	n/a	chr12:48222745-48222754
13	POLR2A	chr12:48222459-48223562	K562	blood:	n/a	n/a
14	POLR2A	chr12:48222173-48223698	K562	blood:	n/a	n/a
15	EGR1	chr12:48222717-48223587	HCT-116	colon:	n/a	chr12:48223198-48223213 chr12:48223201-48223211 chr12:48223200-48223211 chr12:48223201-48223211 chr12:48223199-48223212 chr12:48223200-48223211 chr12:48223199-48223212 chr12:48223199-48223213 chr12:48223195-48223217
16	TAL1	chr12:48223451-48223767	K562	blood:	n/a	chr12:48223522-48223537
17	JUND	chr12:48222698-48223590	K562	blood:	n/a	chr12:48222745-48222754
18	RCOR1	chr12:48222684-48223591	K562	blood:	n/a	n/a
19	RCOR1	chr12:48222494-48223563	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48223218..48223733-chr16:30076666..30077343,2	Hela-S3	cervix:
2	chr12:48222905..48223893-chr2:97202019..97202875,2	Hela-S3	cervix:
3	chr12:48098907..48100853-chr12:48223145..48224856,2	MCF-7	breast:
4	chr12:48221119..48223794-chr12:48297710..48299941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257488	TF binding region
ENSG00000005175	Chromatin interaction
ENSG00000196843	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000149925	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11168256	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11168257	0.84[AMR][1000 genomes]
rs11168258	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12721362	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487602	0.83[AMR][1000 genomes]
rs7487637	0.83[AMR][1000 genomes]
rs7973956	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48214400-48226400	Enhancers	Primary T cells fromperipheralblood	blood
2	chr12:48215000-48224600	Enhancers	Primary T cells from cord blood	blood
3	chr12:48215000-48224800	Enhancers	Fetal Muscle Leg	muscle
4	chr12:48215200-48223800	Enhancers	Adipose Nuclei	Adipose
5	chr12:48215200-48224800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:48215800-48224200	Enhancers	NHDF-Ad	bronchial
7	chr12:48216000-48223600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:48217000-48226200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr12:48218000-48223600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:48218200-48225800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:48218400-48225800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:48218600-48224800	Enhancers	Thymus	Thymus
13	chr12:48218600-48226400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:48218800-48223600	Enhancers	Placenta	Placenta
15	chr12:48218800-48223800	Enhancers	Fetal Muscle Trunk	muscle
16	chr12:48218800-48226400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:48218800-48229000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:48219000-48223600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:48219000-48228800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:48220000-48223600	Enhancers	Lung	lung
21	chr12:48220000-48226200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:48220800-48226800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:48221200-48223600	Enhancers	Fetal Heart	heart
24	chr12:48221800-48223600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:48221800-48224200	Enhancers	Spleen	Spleen
26	chr12:48221800-48224400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:48221800-48224400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr12:48221800-48224400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:48221800-48224600	Enhancers	Left Ventricle	heart
30	chr12:48221800-48226800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:48222000-48223600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:48222000-48223600	Enhancers	Fetal Lung	lung
33	chr12:48222000-48223600	Enhancers	Gastric	stomach
34	chr12:48222000-48223600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr12:48222000-48223600	Enhancers	Right Atrium	heart
36	chr12:48222000-48223600	Enhancers	HUVEC	blood vessel
37	chr12:48222000-48223800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:48222000-48224200	Enhancers	HMEC	breast
39	chr12:48222000-48224400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:48222000-48224600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:48222000-48224600	Enhancers	Right Ventricle	heart
42	chr12:48222200-48223600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr12:48222200-48223600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:48222200-48223600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:48222200-48223600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr12:48222200-48223600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:48222200-48223600	Enhancers	Fetal Intestine Large	intestine
48	chr12:48222200-48223600	Enhancers	Fetal Intestine Small	intestine
49	chr12:48222200-48223600	Enhancers	Fetal Stomach	stomach
50	chr12:48222200-48223600	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links