Variant report

Variant	rs11171760
Chromosome Location	chr12:56554246-56554247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:130)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:130 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56551094-56558885	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:56554227-56556989	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56551096-56559842	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56551899-56559978	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:56551937-56557019	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:56554034-56554275	A549	lung:	n/a	n/a
7	POLR2A	chr12:56550969-56558589	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:56551944-56557093	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:56551911-56556101	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:56551250-56558611	U87	brain:	n/a	n/a
11	PBX3	chr12:56553571-56556173	SK-N-SH	brain:	n/a	n/a
12	JUN	chr12:56554170-56554535	HUVEC	blood vessel:	n/a	n/a
13	BCL3	chr12:56554195-56554578	GM12878	blood:	n/a	chr12:56554315-56554324
14	JUND	chr12:56552646-56555329	A549	lung:	n/a	n/a
15	POLR2A	chr12:56551168-56556161	H1-hESC	embryonic stem cell:	n/a	n/a
16	RUNX3	chr12:56554033-56554619	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:56551896-56556539	HCT-116	colon:	n/a	n/a
18	POLR2A	chr12:56551408-56556564	K562	blood:	n/a	n/a
19	POLR2A	chr12:56550856-56557007	HepG2	liver:	n/a	n/a
20	CHD1	chr12:56551947-56555381	IMR90	lung:	n/a	chr12:56552251-56552261 chr12:56554880-56554890
21	POLR2A	chr12:56551369-56560498	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:56551123-56558578	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:56551053-56559864	GM12891	blood:	n/a	n/a
24	POLR2A	chr12:56551393-56557009	K562	blood:	n/a	n/a
25	CHD1	chr12:56554178-56554608	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:56550960-56557121	K562	blood:	n/a	n/a
27	BCL3	chr12:56551157-56556978	A549	lung:	n/a	chr12:56553213-56553222 chr12:56554315-56554324 chr12:56552652-56552661 chr12:56554170-56554179
28	POLR2A	chr12:56551331-56558611	U87	brain:	n/a	n/a
29	POLR2A	chr12:56551292-56558563	HepG2	liver:	n/a	n/a
30	MYC	chr12:56554218-56554389	HUVEC	blood vessel:	n/a	n/a
31	PML	chr12:56554228-56554689	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:56550957-56556171	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:56551237-56556498	GM12878	blood:	n/a	n/a
34	STAT5A	chr12:56554058-56554489	GM12878	blood:	n/a	chr12:56554343-56554355
35	POLR2A	chr12:56551288-56555232	K562	blood:	n/a	n/a
36	POLR2A	chr12:56553671-56554519	A549	lung:	n/a	n/a
37	POLR2A	chr12:56553459-56557519	K562	blood:	n/a	n/a
38	FOXM1	chr12:56553557-56554471	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:56551184-56558544	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:56550944-56560010	GM12892	blood:	n/a	n/a
41	POLR2A	chr12:56550950-56560311	U87	brain:	n/a	n/a
42	POLR2A	chr12:56550946-56559901	GM12892	blood:	n/a	n/a
43	ATF2	chr12:56554061-56554534	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:56553575-56555357	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr12:56550849-56560509	H1-hESC	embryonic stem cell:	n/a	n/a
46	PML	chr12:56553623-56554920	K562	blood:	n/a	chr12:56554129-56554137
47	POLR2A	chr12:56551127-56558589	GM18505	blood:	n/a	n/a
48	POLR2A	chr12:56551356-56556024	K562	blood:	n/a	n/a
49	POLR2A	chr12:56551464-56559788	HUVEC	blood vessel:	n/a	n/a
50	CTCF	chr12:56554160-56554310	HUVEC	blood vessel:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
2	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
3	chr12:56121253..56122830-chr12:56553054..56555339,2	MCF-7	breast:
4	chr12:56434567..56436421-chr12:56551645..56554362,3	MCF-7	breast:
5	chr12:56551311..56554280-chr12:56613250..56616267,3	MCF-7	breast:
6	chr12:56531568..56534983-chr12:56550075..56554520,6	MCF-7	breast:
7	chr12:56516279..56526040-chr12:56550254..56554953,37	MCF-7	breast:
8	chr12:56549760..56554422-chr12:56650832..56654963,6	MCF-7	breast:
9	chr12:56536501..56538802-chr12:56552198..56554579,2	MCF-7	breast:
10	chr12:56529351..56534783-chr12:56551483..56555184,6	MCF-7	breast:
11	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
12	chr12:56497819..56500036-chr12:56550546..56554351,4	MCF-7	breast:
13	chr12:56108963..56111189-chr12:56554025..56556182,2	MCF-7	breast:
14	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
15	chr12:56551730..56554656-chr12:57027945..57032236,3	K562	blood:
16	chr12:56223309..56224865-chr12:56552081..56554400,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257809	TF binding region
MYL6	TF binding region
ENSG00000135392	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135441	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000258311	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000257449	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11837267	1.00[EUR][1000 genomes]
rs12298822	1.00[EUR][1000 genomes]
rs12306670	1.00[EUR][1000 genomes]
rs12308473	1.00[EUR][1000 genomes]
rs17852368	1.00[EUR][1000 genomes]
rs2450101	1.00[EUR][1000 genomes]
rs2629453	1.00[EUR][1000 genomes]
rs28546848	1.00[EUR][1000 genomes]
rs56163805	1.00[EUR][1000 genomes]
rs59499104	1.00[EUR][1000 genomes]
rs73340385	1.00[EUR][1000 genomes]
rs73340390	1.00[EUR][1000 genomes]
rs7397951	1.00[EUR][1000 genomes]
rs772925	1.00[EUR][1000 genomes]
rs772926	1.00[EUR][1000 genomes]
rs773654	1.00[EUR][1000 genomes]
rs773663	1.00[EUR][1000 genomes]
rs7967464	1.00[EUR][1000 genomes]
rs7975486	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv559011	chr12:56551249-56555022	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
3	nsv559012	chr12:56551249-56555360	Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv559013	chr12:56551249-56556389	Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv559014	chr12:56551250-56555022	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
6	nsv559015	chr12:56551480-56555022	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 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	chr12:56551000-56554400	Active TSS	Ovary	ovary
2	chr12:56551400-56554400	Active TSS	Small Intestine	intestine
3	chr12:56552200-56555000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:56552200-56555800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr12:56552400-56554400	ZNF genes & repeats	Fetal Heart	heart
6	chr12:56552400-56554600	Transcr. at gene 5' and 3'	Fetal Lung	lung
7	chr12:56552400-56554800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
8	chr12:56552400-56555000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
9	chr12:56552400-56555000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr12:56552400-56555400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
11	chr12:56552600-56555000	Transcr. at gene 5' and 3'	A549	lung
12	chr12:56552600-56555200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:56552600-56555600	Transcr. at gene 5' and 3'	HSMM	muscle
14	chr12:56552800-56554600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr12:56552800-56555000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
16	chr12:56552800-56555000	Transcr. at gene 5' and 3'	Thymus	Thymus
17	chr12:56552800-56555400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
18	chr12:56552800-56555800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:56552800-56556000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
20	chr12:56552800-56556200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:56553000-56554400	Transcr. at gene 5' and 3'	K562	blood
22	chr12:56553000-56554600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:56553000-56554600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
24	chr12:56553000-56555000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
25	chr12:56553000-56555000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
26	chr12:56553000-56555200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:56553000-56555200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
28	chr12:56553000-56555400	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr12:56553000-56555600	Transcr. at gene 5' and 3'	NHEK	skin
30	chr12:56553000-56555600	Transcr. at gene 5' and 3'	NHLF	lung
31	chr12:56553000-56555600	Transcr. at gene 5' and 3'	Osteobl	bone
32	chr12:56553000-56555800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:56553000-56556200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
34	chr12:56553000-56557000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
35	chr12:56553200-56554400	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
36	chr12:56553200-56554400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:56553200-56554400	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
38	chr12:56553200-56554400	Transcr. at gene 5' and 3'	Spleen	Spleen
39	chr12:56553200-56554600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
40	chr12:56553200-56554600	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:56553200-56554800	Transcr. at gene 5' and 3'	Placenta	Placenta
42	chr12:56553200-56554800	Transcr. at gene 5' and 3'	Stomach Mucosa	stomach
43	chr12:56553200-56554800	Transcr. at gene 5' and 3'	HepG2	liver
44	chr12:56553200-56555000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:56553200-56555000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr12:56553200-56555000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
47	chr12:56553200-56555000	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:56553200-56555000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
49	chr12:56553200-56555000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:56553200-56555200	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links