Variant report

Variant	rs56007407
Chromosome Location	chr2:56413246-56413247
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	REST	chr2:56412224-56413569	H1-neurons	neurons:	n/a	chr2:56413204-56413224 chr2:56412496-56412509
2	POLR2A	chr2:56412167-56413464	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:56412732-56413266	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr2:56412293-56413258	H1-neurons	neurons:	n/a	n/a
5	GABPA	chr2:56412553-56413280	MCF-7	breast:	n/a	n/a
6	POLR2A	chr2:56412317-56413277	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr2:56412177-56413291	HUVEC	blood vessel:	n/a	n/a
8	TEAD4	chr2:56412765-56413269	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:56410759-56413309	HUVEC	blood vessel:	n/a	n/a
10	ZNF263	chr2:56410709-56413339	HEK293-T-REx	kidney:	n/a	chr2:56412088-56412097
11	TEAD4	chr2:56412815-56413277	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:56412325-56413344	ProgFib	skin:	n/a	n/a
13	POLR2A	chr2:56412303-56413337	HUVEC	blood vessel:	n/a	n/a
14	CTBP2	chr2:56410673-56413313	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:56412138-56413547	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:56410584-56413719	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000233251	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10490395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10490396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10490398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10490399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190051	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17190058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190121	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17190170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17268619	1.00[AFR][1000 genomes]
rs17268653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17268688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17268695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55644642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56017486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56207598	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801150	1.00[AFR][1000 genomes]
rs72801161	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801179	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801180	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72801189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72801196	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72801200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72803004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72803010	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72803016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2762648	chr2:56386656-56422448	Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56410600-56413400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr2:56410600-56413400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:56410600-56413400	Active TSS	Brain Hippocampus Middle	brain
4	chr2:56410600-56413400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:56410600-56413600	Active TSS	Psoas Muscle	Psoas
6	chr2:56410600-56413600	Active TSS	Right Atrium	heart
7	chr2:56410800-56413400	Active TSS	Left Ventricle	heart
8	chr2:56410800-56413600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr2:56412200-56413400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
10	chr2:56412200-56413400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
11	chr2:56412200-56413400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
12	chr2:56412200-56413600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr2:56412400-56413400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:56412600-56413400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:56412600-56413400	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr2:56412600-56413400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
17	chr2:56413000-56413400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
18	chr2:56413000-56413400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:56413000-56413400	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr2:56413000-56413400	Bivalent Enhancer	Fetal Kidney	kidney
21	chr2:56413000-56413400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
22	chr2:56413000-56413400	Flanking Active TSS	HSMMtube	muscle
23	chr2:56413000-56413600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr2:56413000-56413600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
25	chr2:56413000-56413600	Transcr. at gene 5' and 3'	HSMM	muscle
26	chr2:56413000-56413600	Flanking Active TSS	HUVEC	blood vessel
27	chr2:56413200-56413400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr2:56413200-56413400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
29	chr2:56413200-56413400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:56413200-56413400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:56413200-56413400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:56413200-56413400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
33	chr2:56413200-56413400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr2:56413200-56413400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:56413200-56413400	Flanking Active TSS	Brain Angular Gyrus	brain
36	chr2:56413200-56413400	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr2:56413200-56413400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr2:56413200-56413400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
39	chr2:56413200-56413400	Bivalent Enhancer	Fetal Stomach	stomach
40	chr2:56413200-56413600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr2:56413200-56413600	Bivalent Enhancer	Fetal Brain Male	brain
42	chr2:56413200-56413600	Enhancers	Fetal Heart	heart
43	chr2:56413200-56413600	Enhancers	Lung	lung
44	chr2:56413200-56413800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:56413200-56419600	Weak transcription	Placenta	Placenta
46	chr2:56413200-56419800	Weak transcription	Right Ventricle	heart

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