Variant report

Variant	rs55658978
Chromosome Location	chr11:56947190-56947191
allele	C/T
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	CTBP2	chr11:56947016-56949186	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3A	chr11:56947163-56947934	H1-hESC	embryonic stem cell:	n/a	chr11:56947890-56947899
3	REST	chr11:56947182-56948253	H1-neurons	neurons:	n/a	chr11:56947456-56947474 chr11:56947915-56947928 chr11:56947782-56947795 chr11:56947911-56947931
4	ZNF143	chr11:56947186-56948247	H1-hESC	embryonic stem cell:	n/a	chr11:56947765-56947783

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:56945716..56947687-chr11:56952025..56954655,2	K562	blood:
2	chr11:56946370..56948285-chr11:56958607..56960284,2	MCF-7	breast:

Variant related genes	Relation type
LRRC55	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1941036	0.82[ASN][1000 genomes]
rs55788532	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6591408	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv12593	chr11:56946787-56948827	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56946200-56947800	Enhancers	Fetal Brain Male	brain
2	chr11:56946400-56947400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:56946600-56947200	Flanking Active TSS	Fetal Brain Female	brain
4	chr11:56946600-56948600	Enhancers	Pancreas	Pancrea
5	chr11:56946800-56947200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr11:56946800-56947200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
7	chr11:56946800-56947200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:56946800-56947200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:56946800-56948600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:56947000-56947200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr11:56947000-56947200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:56947000-56947200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr11:56947000-56947200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr11:56947000-56947200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr11:56947000-56947200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:56947000-56947200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:56947000-56947200	Bivalent Enhancer	Brain Germinal Matrix	brain
18	chr11:56947000-56947400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:56947000-56947400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:56947000-56947400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:56947000-56947600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr11:56947000-56947800	Bivalent Enhancer	Fetal Stomach	stomach
23	chr11:56947000-56948200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr11:56947000-56948400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr11:56947000-56948400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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