Variant report

Variant	rs73105847
Chromosome Location	chr12:48138283-48138284
allele	G/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	ZEB1	chr12:48137686-48138286	HepG2	liver:	n/a	chr12:48137991-48138002 chr12:48138001-48138013 chr12:48137990-48137999 chr12:48138003-48138012 chr12:48137990-48138002
2	RAD21	chr12:48137723-48138339	MCF-7	breast:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
3	RAD21	chr12:48137715-48138302	ECC-1	luminal epithelium:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
4	POLR2A	chr12:48138236-48139493	ECC-1	luminal epithelium:	n/a	n/a
5	ZNF263	chr12:48137574-48139188	HEK293-T-REx	kidney:	n/a	chr12:48138893-48138914
6	CTCF	chr12:48137746-48138335	A549	lung:	n/a	chr12:48137967-48137976 chr12:48137964-48137982 chr12:48137966-48137987 chr12:48137967-48137980
7	RCOR1	chr12:48137900-48138473	K562	blood:	n/a	n/a
8	TEAD4	chr12:48137724-48138338	ECC-1	luminal epithelium:	n/a	n/a
9	ZEB1	chr12:48137678-48138334	HepG2	liver:	n/a	chr12:48137991-48138002 chr12:48138001-48138013 chr12:48137990-48137999 chr12:48138003-48138012 chr12:48137990-48138002
10	STAT3	chr12:48138279-48138318	MCF10A-Er-Src	breast:	n/a	n/a
11	SMC3	chr12:48137653-48138349	SK-N-SH	brain:	n/a	chr12:48137966-48137980
12	CTCF	chr12:48137632-48138289	MCF-7	breast:	n/a	chr12:48137967-48137976 chr12:48137964-48137982 chr12:48137966-48137987 chr12:48137967-48137980
13	ZNF143	chr12:48137819-48138321	GM12878	blood:	n/a	n/a
14	RAD21	chr12:48137524-48138418	HCT-116	colon:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
15	CTCF	chr12:48138280-48138430	GM12872	blood:	n/a	n/a
16	ZNF143	chr12:48137812-48138464	K562	blood:	n/a	n/a
17	CTCF	chr12:48137518-48138428	HCT-116	colon:	n/a	chr12:48137967-48137976 chr12:48137964-48137982 chr12:48137966-48137987 chr12:48137967-48137980
18	RAD21	chr12:48137595-48138475	HCT-116	colon:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
19	CTCF	chr12:48138260-48138410	GM06990	blood:	n/a	n/a
20	RAD21	chr12:48134688-48138386	SK-N-SH	brain:	n/a	chr12:48137969-48137978 chr12:48136189-48136201 chr12:48136184-48136203 chr12:48137970-48137982 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48137965-48137984 chr12:48136187-48136200 chr12:48137968-48137981
21	RAD21	chr12:48137682-48138284	H1-hESC	embryonic stem cell:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
22	RAD21	chr12:48137747-48138285	A549	lung:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
23	RAD21	chr12:48137716-48138522	ECC-1	luminal epithelium:	n/a	chr12:48137969-48137978 chr12:48137970-48137982 chr12:48137965-48137984 chr12:48137968-48137981
24	RCOR1	chr12:48137930-48138378	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48137300..48138425-chr12:48152736..48153859,11	MCF-7	breast:
2	chr12:48135903..48138754-chr12:48165575..48168395,4	MCF-7	breast:
3	chr12:48108807..48109517-chr12:48137483..48138335,4	MCF-7	breast:
4	chr12:48137535..48138497-chr12:48172832..48173710,7	MCF-7	breast:
5	chr12:48134835..48139182-chr12:48152118..48155732,5	MCF-7	breast:
6	chr12:48136388..48139799-chr12:48164464..48168424,4	K562	blood:
7	chr12:48111026..48111953-chr12:48137523..48138379,2	MCF-7	breast:
8	chr12:48137485..48138437-chr12:48232236..48232936,5	MCF-7	breast:
9	chr12:48137571..48138453-chr12:48160089..48161617,7	MCF-7	breast:
10	chr12:48137493..48138878-chr12:48152464..48153861,18	MCF-7	breast:
11	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:
12	chr12:48136735..48141051-chr12:48142699..48146079,6	K562	blood:

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111405	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12423045	1.00[AFR][1000 genomes]
rs12425816	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35784744	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57848393	1.00[ASN][1000 genomes]
rs60186089	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67201012	1.00[ASN][1000 genomes]
rs67408202	1.00[ASN][1000 genomes]
rs73104138	1.00[AFR][1000 genomes]
rs73104143	1.00[AFR][1000 genomes]
rs73104148	1.00[AFR][1000 genomes]
rs73104152	1.00[AFR][1000 genomes]
rs73104155	1.00[AFR][1000 genomes]
rs73104161	1.00[AFR][1000 genomes]
rs73104163	1.00[AFR][1000 genomes]
rs73104177	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73104184	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73104188	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73104190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73104197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105803	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105812	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105814	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105819	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
5	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
7	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
8	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:48131800-48141000	Weak transcription	Gastric	stomach
10	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:48134400-48138600	Weak transcription	K562	blood
12	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
13	chr12:48135000-48145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:48135200-48138600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48135200-48140200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:48135400-48139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:48135400-48139800	Weak transcription	Ovary	ovary
18	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
19	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:48135600-48138800	Weak transcription	Fetal Lung	lung
21	chr12:48135600-48138800	Weak transcription	Right Atrium	heart
22	chr12:48135600-48139600	Weak transcription	Lung	lung
23	chr12:48135600-48140400	Weak transcription	Esophagus	oesophagus
24	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:48135800-48138800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:48135800-48139800	Weak transcription	Spleen	Spleen
27	chr12:48135800-48140200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:48135800-48140600	Weak transcription	HUVEC	blood vessel
29	chr12:48135800-48145400	Weak transcription	NHDF-Ad	bronchial
30	chr12:48136000-48139400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:48136000-48139600	Weak transcription	Primary B cells from cord blood	blood
32	chr12:48136000-48146200	Weak transcription	Osteobl	bone
33	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:48136200-48138400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:48136400-48138600	Weak transcription	Brain Angular Gyrus	brain
36	chr12:48136400-48138600	Weak transcription	Fetal Heart	heart
37	chr12:48136400-48138800	Weak transcription	Left Ventricle	heart
38	chr12:48136400-48139000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:48136400-48140400	Weak transcription	Placenta	Placenta
40	chr12:48136600-48138800	Weak transcription	Brain Anterior Caudate	brain
41	chr12:48136600-48139400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:48136600-48140400	Weak transcription	Stomach Mucosa	stomach
43	chr12:48136600-48142400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:48137000-48139800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:48137200-48139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:48137400-48138600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:48137400-48139800	Enhancers	Brain Hippocampus Middle	brain
48	chr12:48137400-48142000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48137600-48138400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr12:48137600-48138400	Weak transcription	Brain Substantia Nigra	brain

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