Variant report

Variant	rs28561651
Chromosome Location	chr11:77181378-77181379
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	MTA3	chr11:77181213-77182814	GM12878	blood:	n/a	n/a
2	NFIC	chr11:77181329-77181986	GM12878	blood:	n/a	n/a
3	BCLAF1	chr11:77181348-77181937	GM12878	blood:	n/a	chr11:77181678-77181687 chr11:77181640-77181649

No.	Distal block	Cell Line	Cell type
1	chr11:77179858..77182882-chr11:77183387..77186511,3	MCF-7	breast:
2	chr11:77168519..77171597-chr11:77180665..77182753,3	MCF-7	breast:
3	chr11:77172481..77174902-chr11:77181213..77184183,2	MCF-7	breast:

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

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1453342	0.80[EUR][1000 genomes]
rs17135578	0.80[EUR][1000 genomes]
rs17135582	0.80[EUR][1000 genomes]
rs17135589	0.80[EUR][1000 genomes]
rs17135598	0.80[EUR][1000 genomes]
rs28418374	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58956786	0.80[EUR][1000 genomes]
rs59602069	0.80[EUR][1000 genomes]
rs59695040	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][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:52 , 50 per page) page: 1 2

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	chr11:77178200-77181400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:77178200-77181400	Enhancers	Duodenum Mucosa	Duodenum
10	chr11:77178200-77181400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr11:77178200-77182800	Enhancers	Fetal Intestine Large	intestine
12	chr11:77178400-77181400	Weak transcription	Colonic Mucosa	Colon
13	chr11:77178400-77182000	Weak transcription	Fetal Brain Male	brain
14	chr11:77178400-77182400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:77178400-77183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:77178400-77183400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:77178800-77182600	Enhancers	Fetal Intestine Small	intestine
18	chr11:77179200-77182400	Weak transcription	Psoas Muscle	Psoas
19	chr11:77179200-77182800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:77179400-77181400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:77179400-77181400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:77179400-77182400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:77179600-77181400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:77179600-77182400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:77179800-77181400	Weak transcription	Brain Substantia Nigra	brain
26	chr11:77179800-77181600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:77179800-77183600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:77180000-77183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:77180200-77181400	Weak transcription	Liver	Liver
30	chr11:77180200-77183400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr11:77180200-77183800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr11:77180400-77181400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:77180400-77181400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr11:77180400-77181600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr11:77180400-77182400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:77180400-77182400	Weak transcription	Ovary	ovary
37	chr11:77180400-77183800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr11:77181000-77181400	Enhancers	Stomach Mucosa	stomach
39	chr11:77181000-77182000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr11:77181000-77182800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:77181000-77183000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:77181000-77183800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr11:77181000-77184200	Enhancers	Dnd41	blood
44	chr11:77181200-77181400	Enhancers	Primary hematopoietic stem cells	blood
45	chr11:77181200-77181400	Active TSS	Monocytes-CD14+_RO01746	blood
46	chr11:77181200-77181600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr11:77181200-77181600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr11:77181200-77182000	Active TSS	GM12878-XiMat	blood
49	chr11:77181200-77182400	Enhancers	Small Intestine	intestine
50	chr11:77181200-77183400	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links