Variant report

Variant	rs74088318
Chromosome Location	chr13:53423334-53423335
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	CTCF	chr13:53423240-53423390	BE2_C	brain:	n/a	n/a
2	POLR2A	chr13:53422422-53423366	H1-neurons	neurons:	n/a	n/a
3	REST	chr13:53422663-53426246	HL-60	blood:	n/a	chr13:53424040-53424053 chr13:53422864-53422877 chr13:53424988-53425001 chr13:53425721-53425731 chr13:53424411-53424421 chr13:53425716-53425729 chr13:53422984-53422998 chr13:53422986-53422996 chr13:53425719-53425733 chr13:53424936-53424945 chr13:53424047-53424057
4	REST	chr13:53422151-53423511	H1-neurons	neurons:	n/a	chr13:53422864-53422877 chr13:53422984-53422998 chr13:53422986-53422996

No.	Distal block	Cell Line	Cell type
1	chr13:53416128..53422445-chr13:53423052..53427915,11	MCF-7	breast:
2	chr13:53422829..53424558-chr13:53771804..53774307,2	MCF-7	breast:
3	chr13:53423269..53426675-chr13:53427472..53433524,8	MCF-7	breast:

Variant related genes	Relation type
PCDH8	TF binding region
ENSG00000225510	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17052613	1.00[AMR][1000 genomes]
rs56217013	1.00[AMR][1000 genomes]
rs56740905	1.00[AMR][1000 genomes]
rs57598135	1.00[AMR][1000 genomes]
rs58545123	1.00[AMR][1000 genomes]
rs58732737	1.00[AMR][1000 genomes]
rs60472137	1.00[AMR][1000 genomes]
rs61141148	1.00[AMR][1000 genomes]
rs74086052	1.00[AMR][1000 genomes]
rs74086055	1.00[AMR][1000 genomes]
rs74086507	1.00[AMR][1000 genomes]
rs74086510	1.00[AMR][1000 genomes]
rs74086511	1.00[AMR][1000 genomes]
rs74086514	1.00[AMR][1000 genomes]
rs74086515	1.00[AMR][1000 genomes]
rs74086517	1.00[AMR][1000 genomes]
rs74086519	1.00[AMR][1000 genomes]
rs74086523	1.00[AMR][1000 genomes]
rs74086527	1.00[AMR][1000 genomes]
rs74088311	1.00[AMR][1000 genomes]
rs74088320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088322	1.00[AMR][1000 genomes]
rs74088323	1.00[AMR][1000 genomes]
rs74088324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088330	1.00[AMR][1000 genomes]
rs74088337	1.00[AMR][1000 genomes]
rs74088339	1.00[AMR][1000 genomes]
rs74088358	1.00[AMR][1000 genomes]
rs74088371	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900089	chr13:53385334-53429453	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1810064	chr13:53412849-53441018	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1822518	chr13:53412849-53441018	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv1829072	chr13:53412849-53441018	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv523092	chr13:53419139-53429453	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53419600-53424400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr13:53420000-53424000	ZNF genes & repeats	GM12878-XiMat	blood
3	chr13:53420800-53423400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:53421000-53423400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
5	chr13:53421200-53424800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr13:53421400-53424400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
7	chr13:53421600-53424400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
8	chr13:53421800-53426200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
9	chr13:53422000-53423400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr13:53422000-53423400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
11	chr13:53422200-53424600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr13:53422400-53424400	Bivalent Enhancer	Fetal Thymus	thymus
13	chr13:53422600-53424400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:53422600-53424600	Weak transcription	Gastric	stomach
15	chr13:53422600-53424800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr13:53422600-53424800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:53422800-53423400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:53422800-53423400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
19	chr13:53422800-53424400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr13:53422800-53424600	Weak transcription	Pancreas	Pancrea
21	chr13:53422800-53424600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
22	chr13:53423000-53423400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:53423000-53423400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:53423000-53423400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:53423000-53423400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
26	chr13:53423000-53423400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
27	chr13:53423000-53423600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:53423000-53423600	Bivalent Enhancer	Fetal Lung	lung
29	chr13:53423000-53423800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr13:53423000-53423800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
31	chr13:53423000-53423800	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
32	chr13:53423000-53423800	Flanking Active TSS	Fetal Brain Male	brain
33	chr13:53423000-53424000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
34	chr13:53423000-53424600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:53423000-53424600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr13:53423000-53424600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr13:53423000-53424600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr13:53423000-53425000	Flanking Active TSS	Fetal Brain Female	brain
39	chr13:53423200-53423400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr13:53423200-53423400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:53423200-53423400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:53423200-53423600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
43	chr13:53423200-53423800	Flanking Bivalent TSS/Enh	Pancreatic Islets	Pancreatic Islet
44	chr13:53423200-53423800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
45	chr13:53423200-53424200	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr13:53423200-53424600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:53423200-53424600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
48	chr13:53423200-53424800	Bivalent Enhancer	Fetal Stomach	stomach

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