Variant report

Variant	rs12295549
Chromosome Location	chr11:119580492-119580493
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	chr11:119580065-119580712	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:119580233-119581383	H1-neurons	neurons:	n/a	n/a
3	MXI1	chr11:119580064-119581705	SK-N-SH	brain:	n/a	chr11:119580568-119580583 chr11:119580570-119580585
4	MXI1	chr11:119580401-119580935	GM12878	blood:	n/a	chr11:119580568-119580583 chr11:119580570-119580585
5	EP300	chr11:119580445-119580539	GM12878	blood:	n/a	n/a
6	SIN3A	chr11:119580402-119580730	H1-hESC	embryonic stem cell:	n/a	n/a
7	MTA3	chr11:119580411-119580827	GM12878	blood:	n/a	n/a
8	MAZ	chr11:119580286-119580638	GM12878	blood:	n/a	chr11:119580570-119580579
9	POLR2A	chr11:119579919-119581093	HL-60	blood:	n/a	n/a
10	EP300	chr11:119580422-119580748	SK-N-SH_RA	brain:	n/a	n/a
11	EP300	chr11:119580401-119580723	SK-N-SH_RA	brain:	n/a	n/a
12	ZNF143	chr11:119580336-119580718	GM12878	blood:	n/a	chr11:119580342-119580361
13	POLR2A	chr11:119580313-119581197	HL-60	blood:	n/a	n/a
14	ZNF143	chr11:119580316-119580743	H1-hESC	embryonic stem cell:	n/a	chr11:119580342-119580361
15	MAX	chr11:119580432-119580767	H1-hESC	embryonic stem cell:	n/a	chr11:119580570-119580579
16	REST	chr11:119580048-119581275	H1-neurons	neurons:	n/a	chr11:119580807-119580817 chr11:119580290-119580298 chr11:119580805-119580819
17	EGR1	chr11:119580395-119580565	GM12878	blood:	n/a	chr11:119580486-119580501 chr11:119580488-119580502
18	POLR2A	chr11:119580396-119581117	H1-neurons	neurons:	n/a	n/a
19	RUNX3	chr11:119580340-119580752	GM12878	blood:	n/a	chr11:119580540-119580555
20	RUNX3	chr11:119580302-119580818	GM12878	blood:	n/a	chr11:119580540-119580555

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:119578331..119580613-chr11:119597735..119601327,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255247	TF binding region
ENSG00000110400	Chromatin interaction
ENSG00000254854	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11217417	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11217424	1.00[AMR][1000 genomes]
rs11217425	1.00[AMR][1000 genomes]
rs4533046	1.00[AMR][1000 genomes]
rs4938714	1.00[AMR][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	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv468880	chr11:119564496-119588062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv556471	chr11:119564496-119588062	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1051769	chr11:119572865-119630769	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119561000-119580600	Weak transcription	Fetal Kidney	kidney
2	chr11:119565200-119582600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:119568000-119580600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:119568400-119580600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:119568400-119587000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:119568600-119580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:119568600-119580600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:119568600-119590400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:119572600-119592000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:119573000-119591800	Weak transcription	Left Ventricle	heart
11	chr11:119573200-119580600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:119574000-119583200	Weak transcription	Placenta	Placenta
13	chr11:119574000-119597200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:119575200-119591600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:119576000-119580600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:119576800-119580600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:119576800-119587200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:119577000-119581400	Enhancers	Brain Substantia Nigra	brain
19	chr11:119577400-119583000	Weak transcription	Fetal Heart	heart
20	chr11:119577600-119582400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr11:119577800-119583400	Weak transcription	Stomach Mucosa	stomach
22	chr11:119578000-119582400	Weak transcription	Pancreas	Pancrea
23	chr11:119578000-119583600	Weak transcription	Gastric	stomach
24	chr11:119578000-119584800	Weak transcription	Right Ventricle	heart
25	chr11:119578200-119581200	Weak transcription	HepG2	liver
26	chr11:119578400-119580600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr11:119578600-119580600	Enhancers	Fetal Brain Male	brain
28	chr11:119578600-119580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr11:119579000-119581000	Genic enhancers	Esophagus	oesophagus
30	chr11:119579000-119581400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:119579200-119581200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr11:119579400-119581000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:119579400-119581000	Enhancers	Fetal Thymus	thymus
34	chr11:119579400-119581400	Enhancers	HMEC	breast
35	chr11:119579400-119581800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:119579600-119580800	Enhancers	Primary hematopoietic stem cells	blood
37	chr11:119579600-119580800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:119579600-119580800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr11:119579600-119581000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr11:119579600-119581000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:119579600-119581000	Enhancers	Thymus	Thymus
42	chr11:119579600-119581000	Enhancers	HSMMtube	muscle
43	chr11:119579600-119581200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:119579600-119581400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:119579600-119589200	Genic enhancers	Fetal Intestine Small	intestine
46	chr11:119579800-119580600	Enhancers	Brain Cingulate Gyrus	brain
47	chr11:119579800-119580600	Enhancers	Fetal Muscle Leg	muscle
48	chr11:119579800-119580800	Enhancers	Primary B cells from cord blood	blood
49	chr11:119579800-119581000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr11:119579800-119581000	Enhancers	Monocytes-CD14+_RO01746	blood

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