Variant report

Variant	rs4774617
Chromosome Location	chr15:52553744-52553745
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	SIN3A	chr15:52553647-52554451	H1-hESC	embryonic stem cell:	n/a	chr15:52554323-52554332
2	POLR2A	chr15:52553461-52554473	H1-hESC	embryonic stem cell:	n/a	n/a
3	RELA	chr15:52553701-52554665	GM19099	blood:	n/a	n/a
4	CTCF	chr15:52553680-52553830	GM12873	blood:	n/a	n/a
5	RELA	chr15:52553579-52554954	GM18951	blood:	n/a	n/a
6	POLR2A	chr15:52553245-52554572	GM12878	blood:	n/a	n/a
7	SMARCB1	chr15:52553211-52554292	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:52553614-52555009	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr15:52553569-52554844	H1-neurons	neurons:	n/a	n/a
10	TFAP2C	chr15:52553648-52554415	Hela-S3	cervix:	n/a	chr15:52554116-52554131
11	EBF1	chr15:52553655-52553911	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:52553692-52554362	Hela-S3	cervix:	n/a	n/a
13	MAX	chr15:52553696-52554444	GM12878	blood:	n/a	chr15:52554144-52554153
14	MTA3	chr15:52553684-52554435	GM12878	blood:	n/a	n/a
15	SRF	chr15:52553706-52554632	MCF-7	breast:	n/a	chr15:52554235-52554246 chr15:52554231-52554249 chr15:52554234-52554247 chr15:52554232-52554249 chr15:52554234-52554247 chr15:52554235-52554249 chr15:52554236-52554245 chr15:52554232-52554250 chr15:52554236-52554247 chr15:52554234-52554245 chr15:52554233-52554248
16	POLR2A	chr15:52553338-52554291	H1-hESC	embryonic stem cell:	n/a	n/a
17	BHLHE40	chr15:52553726-52554525	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:52553736-52555056	GM12892	blood:	n/a	n/a
19	POLR2A	chr15:52552933-52555124	H1-hESC	embryonic stem cell:	n/a	n/a
20	EBF1	chr15:52553616-52554471	GM12878	blood:	n/a	n/a
21	TCF7L2	chr15:52553733-52554413	Hela-S3	cervix:	n/a	n/a
22	PAX5	chr15:52553646-52554489	GM12878	blood:	n/a	chr15:52553681-52553690
23	POLR2A	chr15:52553479-52554485	GM12892	blood:	n/a	n/a
24	SMARCC1	chr15:52553744-52554876	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr15:52553737-52554669	ECC-1	luminal epithelium:	n/a	chr15:52553787-52553794
26	EBF1	chr15:52553675-52554417	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:52553245-52555031	GM12892	blood:	n/a	n/a
28	FOXM1	chr15:52553623-52554557	GM12878	blood:	n/a	n/a
29	EP300	chr15:52553741-52554665	ECC-1	luminal epithelium:	n/a	n/a
30	TAF1	chr15:52553736-52554287	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr15:52553682-52554406	H1-hESC	embryonic stem cell:	n/a	n/a
32	TCF12	chr15:52553609-52554769	ECC-1	luminal epithelium:	n/a	chr15:52553787-52553794

No.	Distal block	Cell Line	Cell type
1	chr15:52552685..52555324-chr15:52573608..52576301,2	MCF-7	breast:
2	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
3	chr15:52551438..52553868-chr15:52559425..52562079,2	K562	blood:
4	chr15:52545028..52546786-chr15:52553340..52555593,3	MCF-7	breast:
5	chr15:52536643..52538953-chr15:52552429..52555454,3	MCF-7	breast:
6	chr15:52539435..52542328-chr15:52552750..52555467,4	MCF-7	breast:
7	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
8	chr15:52553415..52555370-chr15:52556618..52558914,2	MCF-7	breast:
9	chr14:73602910..73603586-chr15:52553490..52554345,2	Hela-S3	cervix:

Variant related genes	Relation type
MYO5C	TF binding region
ENSG00000080815	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10851510	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10851511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070886	0.81[CHB][hapmap]
rs11070890	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17707198	1.00[CEU][hapmap]
rs3794551	0.81[CHB][hapmap]
rs4432216	1.00[CEU][hapmap]
rs4496072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514621	1.00[CEU][hapmap]
rs4776031	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58479271	1.00[EUR][1000 genomes]
rs59060156	1.00[EUR][1000 genomes]
rs59211915	0.84[EUR][1000 genomes]
rs61367038	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61551630	0.92[EUR][1000 genomes]
rs7165256	0.81[CHB][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7165320	0.82[GIH][hapmap];1.00[TSI][hapmap]
rs7172236	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180204	0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap]
rs9806461	1.00[EUR][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	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52525800-52554000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:52536200-52553800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:52538000-52554600	Weak transcription	Colonic Mucosa	Colon
5	chr15:52540000-52553800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:52542400-52553800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:52543600-52555400	Weak transcription	Liver	Liver
8	chr15:52546800-52553800	Weak transcription	Esophagus	oesophagus
9	chr15:52547000-52555800	Weak transcription	Fetal Intestine Large	intestine
10	chr15:52547600-52553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:52549000-52553800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:52549000-52557800	Weak transcription	Fetal Brain Male	brain
13	chr15:52549200-52553800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:52549200-52554000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:52549400-52554000	Weak transcription	Fetal Lung	lung
16	chr15:52549400-52567200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:52549600-52553800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:52549600-52553800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:52549600-52557400	Weak transcription	Thymus	Thymus
20	chr15:52549800-52553800	Weak transcription	Primary T cells from cord blood	blood
21	chr15:52549800-52554200	Weak transcription	A549	lung
22	chr15:52550000-52553800	Weak transcription	Brain Substantia Nigra	brain
23	chr15:52550000-52554000	Weak transcription	HSMM	muscle
24	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
25	chr15:52550200-52553800	Weak transcription	Left Ventricle	heart
26	chr15:52550200-52554000	Weak transcription	NHLF	lung
27	chr15:52550200-52554600	Weak transcription	Right Ventricle	heart
28	chr15:52550200-52572200	Strong transcription	HepG2	liver
29	chr15:52550400-52553800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:52550400-52554000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:52550600-52553800	Weak transcription	NHDF-Ad	bronchial
32	chr15:52550600-52553800	Weak transcription	Osteobl	bone
33	chr15:52550600-52554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:52550600-52554200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:52550800-52553800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:52550800-52554800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:52551800-52554600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:52552000-52554000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:52552200-52557200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:52552600-52554000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52552800-52556000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr15:52553000-52555000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:52553000-52555000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:52553000-52555400	Enhancers	Primary B cells from peripheral blood	blood
45	chr15:52553000-52556000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:52553000-52556200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr15:52553000-52556400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52553000-52556400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr15:52553000-52562600	Strong transcription	Fetal Intestine Small	intestine
50	chr15:52553200-52553800	Enhancers	HUES6 Cell Line	embryonic stem cell

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