Variant report

Variant	rs73338249
Chromosome Location	chr12:58153961-58153962
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	chr12:58153729-58155164	PFSK-1	brain:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
2	REST	chr12:58153719-58154739	PFSK-1	brain:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
3	POLR2A	chr12:58153851-58153983	GM12878	blood:	n/a	n/a
4	REST	chr12:58153780-58154941	HL-60	blood:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
5	REST	chr12:58153649-58155055	ECC-1	luminal epithelium:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
6	REST	chr12:58153866-58154787	K562	blood:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
7	POLR2A	chr12:58151449-58154225	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:58152625-58154015	K562	blood:	n/a	n/a
9	POLR2A	chr12:58151613-58154807	MCF10A-Er-Src	breast:	n/a	n/a
10	REST	chr12:58153893-58154665	SK-N-SH	brain:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154363-58154372 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
11	REST	chr12:58153891-58154741	PANC-1	pancreas:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
12	CTCF	chr12:58153820-58153970	HepG2	liver:	n/a	n/a
13	REST	chr12:58153913-58154835	H1-hESC	embryonic stem cell:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
14	POLR2A	chr12:58151761-58154012	Hela-S3	cervix:	n/a	n/a
15	REST	chr12:58153797-58154908	ECC-1	luminal epithelium:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
16	REST	chr12:58153919-58154816	A549	lung:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377
17	POLR2A	chr12:58153840-58154005	K562	blood:	n/a	n/a
18	REST	chr12:58153872-58154927	MCF-7	breast:	n/a	chr12:58154361-58154374 chr12:58154364-58154378 chr12:58154719-58154739 chr12:58154363-58154372 chr12:58154719-58154739 chr12:58154358-58154378 chr12:58154358-58154378 chr12:58154359-58154377

No.	Distal block	Cell Line	Cell type
1	chr12:58153606..58155197-chr12:58186466..58188523,2	K562	blood:
2	chr12:57910612..57912523-chr12:58153055..58155888,2	K562	blood:
3	chr12:58153870..58155501-chr12:58325931..58327914,2	K562	blood:
4	chr12:58153738..58156431-chr7:150562978..150565095,2	MCF-7	breast:
5	chr12:58153957..58154503-chr13:53901447..53902222,2	MCF-7	breast:
6	chr12:58109491..58111128-chr12:58152732..58154720,2	K562	blood:
7	chr12:57910530..57914371-chr12:58151795..58155888,4	K562	blood:

Variant related genes	Relation type
CDK4	TF binding region
ENSG00000135506	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs34299538	1.00[AMR][1000 genomes]
rs55849950	1.00[AMR][1000 genomes]
rs56318011	1.00[AMR][1000 genomes]
rs58824032	1.00[AMR][1000 genomes]
rs59476756	1.00[AMR][1000 genomes]
rs73334082	1.00[AMR][1000 genomes]
rs73335910	1.00[AMR][1000 genomes]
rs73338222	1.00[AMR][1000 genomes]
rs73338246	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73338250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73338252	1.00[AMR][1000 genomes]
rs73349954	1.00[AMR][1000 genomes]
rs74094487	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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58150200-58154400	Weak transcription	Psoas Muscle	Psoas
2	chr12:58150400-58158400	Weak transcription	Right Atrium	heart
3	chr12:58150600-58156400	Weak transcription	Small Intestine	intestine
4	chr12:58150600-58156400	Weak transcription	Hela-S3	cervix
5	chr12:58150600-58158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:58150800-58154600	Strong transcription	Fetal Stomach	stomach
7	chr12:58150800-58156200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:58150800-58156800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:58151000-58154000	Strong transcription	Dnd41	blood
10	chr12:58151000-58154600	Weak transcription	Fetal Brain Male	brain
11	chr12:58151000-58154800	Weak transcription	HepG2	liver
12	chr12:58151000-58155400	Strong transcription	Brain Germinal Matrix	brain
13	chr12:58151000-58156000	Strong transcription	Fetal Intestine Small	intestine
14	chr12:58151000-58156600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:58151200-58154000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:58151600-58154000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:58151600-58154000	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:58151600-58154000	Strong transcription	Thymus	Thymus
19	chr12:58151600-58154200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:58151600-58154200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:58151600-58155000	Strong transcription	Primary B cells from cord blood	blood
22	chr12:58151600-58155200	Strong transcription	Primary T cells from cord blood	blood
23	chr12:58151600-58155800	Strong transcription	Fetal Brain Female	brain
24	chr12:58151600-58156400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:58151800-58156200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:58152200-58156600	Weak transcription	Fetal Lung	lung
27	chr12:58152200-58160000	Weak transcription	K562	blood
28	chr12:58152400-58154200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:58152400-58154400	Weak transcription	HMEC	breast
30	chr12:58152400-58154800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:58152400-58156400	Strong transcription	NHEK	skin
32	chr12:58152400-58157400	Weak transcription	HSMMtube	muscle
33	chr12:58152600-58156400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:58152600-58156800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:58152600-58157200	Weak transcription	Liver	Liver
36	chr12:58152800-58154000	Weak transcription	Colonic Mucosa	Colon
37	chr12:58152800-58155200	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:58152800-58156400	Weak transcription	Brain Substantia Nigra	brain
39	chr12:58152800-58158000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:58153000-58154000	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr12:58153000-58154000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr12:58153000-58154000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:58153000-58155000	Weak transcription	Right Ventricle	heart
44	chr12:58153000-58155400	Weak transcription	Ovary	ovary
45	chr12:58153000-58156400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:58153000-58157200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:58153000-58157400	Weak transcription	Pancreas	Pancrea
48	chr12:58153000-58158000	Weak transcription	GM12878-XiMat	blood
49	chr12:58153000-58158200	Weak transcription	Gastric	stomach
50	chr12:58153200-58154000	Enhancers	Primary T helper cells fromperipheralblood	blood

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