Variant report

Variant	rs28497539
Chromosome Location	chr11:77180581-77180582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr11:77180504-77180611	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:77180550-77180600	ProgFib	skin:	n/a
2	chr11:77180550-77180600	ovcar-3	ovarian:	n/a
3	chr11:77180550-77180600	ECC-1	luminal epithelium:	n/a
4	chr11:77180550-77180600	NT2-D1	testis:	n/a
5	chr11:77180550-77180600	HRCEpiC	kidney:	n/a
6	chr11:77180550-77180600	GM12892	blood:	n/a
7	chr11:77180550-77180600	BE2_C	brain:	n/a
8	chr11:77180550-77180600	SKMC	muscle:	n/a
9	chr11:77180550-77180600	PFSK-1	brain:	n/a
10	chr11:77180550-77180600	NHBE	bronchial:	n/a
11	chr11:77180550-77180600	HCM	heart:	n/a
12	chr11:77180550-77180600	K562	blood:	n/a
13	chr11:77180550-77180600	HEEpiC	esophagus:	n/a
14	chr11:77180550-77180600	A549	lung:	n/a
15	chr11:77180550-77180600	HL-60	blood:	n/a
16	chr11:77180550-77180600	GM19239	blood:	n/a
17	chr11:77180550-77180600	SK-N-SH	brain:	n/a
18	chr11:77180550-77180600	AG10803	skin:	n/a
19	chr11:77180550-77180600	RPTEC	kidney:	n/a
20	chr11:77180550-77180600	IMR90	lung:	fetal
21	chr11:77180550-77180600	HepG2	liver:	n/a
22	chr11:77180550-77180600	HNPCEpiC	eye:	n/a
23	chr11:77180550-77180600	GM06990	blood:	n/a
24	chr11:77180550-77180600	GM12878	blood:	n/a
25	chr11:77180550-77180600	NB4	blood:	n/a
26	chr11:77180550-77180600	HAEpiC	amniotic membrane:	n/a
27	chr11:77180550-77180600	AoSMC	blood vessel:	n/a
28	chr11:77180550-77180600	HCT-116	colon:	n/a
29	chr11:77180550-77180600	BJ	skin:	n/a
30	chr11:77180550-77180600	Hepatocyte	liver:	n/a
31	chr11:77180550-77180600	SK-N-MC	brain:	n/a
32	chr11:77180550-77180600	Caco-2	colon:	n/a
33	chr11:77180550-77180600	HPAEpiC	pulmonary alveolar:	n/a
34	chr11:77180550-77180600	AG04450	lung:	fetal
35	chr11:77180550-77180600	H1-hESC	embryonic stem cell:	embryo
36	chr11:77180550-77180600	MCF-7	breast:	n/a
37	chr11:77180550-77180600	NHDF-neo	bronchial:	n/a
38	chr11:77180550-77180600	U87	brain:	n/a
39	chr11:77180550-77180600	AG09319	gingival:	n/a
40	chr11:77180550-77180600	LNCaP	prostate:	n/a
41	chr11:77180550-77180600	HMEC	breast:	n/a
42	chr11:77180550-77180600	HEK293	kidney:	embryo
43	chr11:77180550-77180600	GM12891	blood:	n/a
44	chr11:77180550-77180600	AG09309	skin:	n/a
45	chr11:77180550-77180600	MCF10A-Er-Src	breast:	n/a
46	chr11:77180550-77180600	HRE	kidney:	n/a
47	chr11:77180550-77180600	PANC-1	pancreas:	n/a
48	chr11:77180550-77180600	T-47D	breast:	n/a
49	chr11:77180550-77180600	PrEC	prostate:	n/a
50	chr11:77180550-77180600	Jurkat	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77179858..77182882-chr11:77183387..77186511,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268635	TF binding region
ENSG00000268635	CpG island
ENSG00000268635	Chromatin interaction
ENSG00000149269	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12099425	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:77167800-77182000	Weak transcription	Fetal Kidney	kidney
3	chr11:77169000-77181400	Weak transcription	Brain Angular Gyrus	brain
4	chr11:77171200-77181600	Weak transcription	Primary B cells from cord blood	blood
5	chr11:77173800-77183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:77175400-77181400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:77178000-77181400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr11:77178200-77180600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:77178200-77181000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr11:77178200-77181200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr11:77178200-77181200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr11:77178200-77181400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:77178200-77181400	Enhancers	Duodenum Mucosa	Duodenum
14	chr11:77178200-77181400	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr11:77178200-77182800	Enhancers	Fetal Intestine Large	intestine
16	chr11:77178400-77181400	Weak transcription	Colonic Mucosa	Colon
17	chr11:77178400-77182000	Weak transcription	Fetal Brain Male	brain
18	chr11:77178400-77182400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:77178400-77183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:77178400-77183400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:77178800-77182600	Enhancers	Fetal Intestine Small	intestine
22	chr11:77179200-77180600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:77179200-77182400	Weak transcription	Psoas Muscle	Psoas
24	chr11:77179200-77182800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:77179400-77181400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr11:77179400-77181400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:77179400-77182400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:77179600-77181200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr11:77179600-77181400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:77179600-77182400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:77179800-77181200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr11:77179800-77181400	Weak transcription	Brain Substantia Nigra	brain
33	chr11:77179800-77181600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:77179800-77183600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:77180000-77181000	Weak transcription	Stomach Mucosa	stomach
36	chr11:77180000-77183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:77180200-77181400	Weak transcription	Liver	Liver
38	chr11:77180200-77183400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:77180200-77183800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr11:77180400-77180600	Active TSS	GM12878-XiMat	blood
41	chr11:77180400-77180800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr11:77180400-77181200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr11:77180400-77181200	Weak transcription	Small Intestine	intestine
44	chr11:77180400-77181400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:77180400-77181400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr11:77180400-77181600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr11:77180400-77182400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:77180400-77182400	Weak transcription	Ovary	ovary
49	chr11:77180400-77183800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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