Variant report

Variant	rs12278162
Chromosome Location	chr11:57413165-57413166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57412861-57413489	PANC-1	pancreas:	n/a	n/a
2	TAF7	chr11:57413159-57413603	K562	blood:	n/a	n/a
3	MAZ	chr11:57411935-57413222	IMR90	lung:	n/a	n/a
4	POLR2A	chr11:57411937-57420676	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr11:57413020-57413170	AG10803	skin:	n/a	n/a
7	GTF2B	chr11:57413130-57413485	K562	blood:	n/a	n/a
8	POLR2A	chr11:57413054-57413695	HUVEC	blood vessel:	n/a	n/a
9	BCL3	chr11:57412844-57413298	A549	lung:	n/a	n/a
10	POLR2A	chr11:57412052-57419760	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr11:57412821-57416389	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr11:57411926-57416336	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:57411980-57417263	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr11:57411952-57413217	SK-N-SH	brain:	n/a	chr11:57412446-57412464 chr11:57412441-57412462 chr11:57412448-57412461 chr11:57412447-57412463 chr11:57412452-57412461
17	POLR2A	chr11:57412800-57413590	U87	brain:	n/a	n/a
18	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr11:57412040-57416702	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr11:57412758-57413934	U87	brain:	n/a	n/a
21	POLR2A	chr11:57411922-57418069	SK-N-SH	brain:	n/a	n/a
22	NR2F2	chr11:57412857-57413184	K562	blood:	n/a	n/a
23	ELF1	chr11:57413123-57413485	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:57413075-57413631	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr11:57412961-57418210	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr11:57411868-57413914	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:57412201-57418679	ECC-1	luminal epithelium:	n/a	n/a
28	BRCA1	chr11:57412743-57413173	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr11:57413060-57413210	HBMEC	blood vessel:	n/a	n/a
30	POLR2A	chr11:57410100-57417938	PBDE	blood:	n/a	n/a
31	TBP	chr11:57413152-57413501	K562	blood:	n/a	n/a
32	POLR2A	chr11:57412996-57414001	H1-hESC	embryonic stem cell:	n/a	n/a
33	ATF2	chr11:57412150-57413233	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr11:57412737-57417005	U87	brain:	n/a	n/a
35	POLR2A	chr11:57412808-57413777	HepG2	liver:	n/a	n/a
36	POLR2A	chr11:57412861-57418587	ECC-1	luminal epithelium:	n/a	n/a
37	TBP	chr11:57413108-57414152	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:57412772-57417005	U87	brain:	n/a	n/a
39	POLR2A	chr11:57412977-57416985	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr11:57409804-57420281	PFSK-1	brain:	n/a	n/a
41	ZNF143	chr11:57413084-57413254	K562	blood:	n/a	n/a
42	CTCF	chr11:57413060-57413210	WI-38	lung:	n/a	n/a
43	PML	chr11:57413124-57413706	GM12878	blood:	n/a	n/a
44	ZNF143	chr11:57412963-57413326	H1-hESC	embryonic stem cell:	n/a	n/a
45	CHD2	chr11:57413006-57413662	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57224684..57228396-chr11:57412206..57415806,3	K562	blood:
2	chr11:57334278..57336865-chr11:57411196..57413730,2	K562	blood:
3	chr11:57411538..57415148-chr11:57422707..57424942,3	K562	blood:
4	chr11:57090818..57092799-chr11:57412306..57413962,2	K562	blood:
5	chr11:57191864..57194047-chr11:57412922..57415205,2	K562	blood:
6	chr11:57333866..57335515-chr11:57412954..57415220,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254602	TF binding region
CLP1	TF binding region
ENSG00000172409	Chromatin interaction
ENSG00000134802	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000149115	Chromatin interaction
ENSG00000186907	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11229129	0.84[AFR][1000 genomes]
rs11229138	0.84[AFR][1000 genomes]
rs12269967	1.00[AFR][1000 genomes]
rs12272365	0.84[AFR][1000 genomes]
rs12277841	0.92[AFR][1000 genomes]
rs12286556	0.87[AFR][1000 genomes]
rs12287051	1.00[AFR][1000 genomes]
rs12289980	0.92[AFR][1000 genomes]
rs12292079	0.84[AFR][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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
2	chr11:57408800-57413400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr11:57409000-57413200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:57409000-57414400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:57409000-57416200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:57409200-57413600	Weak transcription	Primary T cells from cord blood	blood
7	chr11:57409600-57413200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:57409600-57413200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:57409600-57413200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:57409600-57413600	Weak transcription	HMEC	breast
11	chr11:57409600-57414000	Weak transcription	Brain Germinal Matrix	brain
12	chr11:57410000-57414200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr11:57410200-57413400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:57411000-57413400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:57411000-57414600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr11:57411200-57413200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:57411200-57413400	Enhancers	Fetal Stomach	stomach
18	chr11:57411200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr11:57411200-57414800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:57411200-57415600	Enhancers	K562	blood
21	chr11:57411400-57413400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:57411400-57413600	Enhancers	Fetal Muscle Leg	muscle
23	chr11:57411400-57413800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr11:57411600-57413400	Enhancers	HSMM	muscle
25	chr11:57411600-57413600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:57411600-57414200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr11:57411600-57414200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr11:57411600-57416200	Enhancers	Fetal Lung	lung
29	chr11:57411800-57413200	Enhancers	NHLF	lung
30	chr11:57411800-57413400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr11:57411800-57413400	Enhancers	Fetal Muscle Trunk	muscle
32	chr11:57412000-57413200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:57412000-57413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:57412000-57413400	Enhancers	Fetal Brain Female	brain
35	chr11:57412000-57413600	Enhancers	Left Ventricle	heart
36	chr11:57412000-57413800	Enhancers	Colon Smooth Muscle	Colon
37	chr11:57412000-57414200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:57412000-57414200	Enhancers	Placenta	Placenta
39	chr11:57412000-57414200	Enhancers	Right Atrium	heart
40	chr11:57412000-57414400	Enhancers	Brain Anterior Caudate	brain
41	chr11:57412000-57414400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr11:57412000-57415800	Enhancers	Placenta Amnion	Placenta Amnion
43	chr11:57412200-57413200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:57412200-57413200	Enhancers	Liver	Liver
45	chr11:57412200-57413200	Enhancers	Brain Hippocampus Middle	brain
46	chr11:57412200-57413400	Enhancers	Primary hematopoietic stem cells	blood
47	chr11:57412200-57413400	Enhancers	Adipose Nuclei	Adipose
48	chr11:57412200-57413400	Enhancers	A549	lung
49	chr11:57412200-57413400	Enhancers	Hela-S3	cervix
50	chr11:57412200-57413400	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links