Variant report

Variant	rs73302698
Chromosome Location	chr12:48138853-48138854
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	TCF7L2	chr12:48138339-48138983	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:48138236-48139493	ECC-1	luminal epithelium:	n/a	n/a
3	ZNF263	chr12:48137574-48139188	HEK293-T-REx	kidney:	n/a	chr12:48138893-48138914
4	ZNF263	chr12:48138360-48139341	K562	blood:	n/a	chr12:48138893-48138914

No.	Distal block	Cell Line	Cell type
1	chr12:48134835..48139182-chr12:48152118..48155732,5	MCF-7	breast:
2	chr12:48136388..48139799-chr12:48164464..48168424,4	K562	blood:
3	chr11:62608633..62609583-chr12:48138415..48139050,2	NB4	blood:
4	chr12:48137493..48138878-chr12:48152464..48153861,18	MCF-7	breast:
5	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:
6	chr12:48136735..48141051-chr12:48142699..48146079,6	K562	blood:

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1859256	0.92[AFR][1000 genomes]
rs56907417	1.00[AMR][1000 genomes]
rs57162394	0.92[AFR][1000 genomes]
rs57691959	0.92[AFR][1000 genomes]
rs58232701	0.92[AFR][1000 genomes]
rs58237186	0.92[AFR][1000 genomes]
rs58280987	0.92[AFR][1000 genomes]
rs58636268	0.91[AFR][1000 genomes]
rs59421933	0.92[AFR][1000 genomes]
rs60608560	0.87[AFR][1000 genomes]
rs61033936	0.92[AFR][1000 genomes]
rs61275291	1.00[AMR][1000 genomes]
rs61288073	0.92[AFR][1000 genomes]
rs61327127	0.89[AFR][1000 genomes]
rs61446607	0.92[AFR][1000 genomes]
rs61709815	1.00[AMR][1000 genomes]
rs61739888	0.92[AFR][1000 genomes]
rs7134842	1.00[AMR][1000 genomes]
rs7300107	0.92[AFR][1000 genomes]
rs7308032	0.98[AFR][1000 genomes]
rs7314320	0.92[AFR][1000 genomes]
rs73302628	0.89[AFR][1000 genomes]
rs73302629	0.92[AFR][1000 genomes]
rs73302650	0.92[AFR][1000 genomes]
rs73302653	0.92[AFR][1000 genomes]
rs73302662	0.92[AFR][1000 genomes]
rs73302664	0.92[AFR][1000 genomes]
rs73302673	0.92[AFR][1000 genomes]
rs73302677	0.92[AFR][1000 genomes]
rs73302679	0.92[AFR][1000 genomes]
rs73302681	0.92[AFR][1000 genomes]
rs73302682	0.92[AFR][1000 genomes]
rs757283	0.92[AFR][1000 genomes]
rs877196	0.92[AFR][1000 genomes]
rs877197	0.92[AFR][1000 genomes]
rs877198	0.92[AFR][1000 genomes]
rs879177	0.92[AFR][1000 genomes]
rs879178	0.89[AFR][1000 genomes]
rs879179	0.92[AFR][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:66 , 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	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
4	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
5	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
6	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:48131800-48141000	Weak transcription	Gastric	stomach
8	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
10	chr12:48135000-48145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:48135200-48140200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:48135400-48139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:48135400-48139800	Weak transcription	Ovary	ovary
14	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
15	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:48135600-48139600	Weak transcription	Lung	lung
17	chr12:48135600-48140400	Weak transcription	Esophagus	oesophagus
18	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:48135800-48139800	Weak transcription	Spleen	Spleen
20	chr12:48135800-48140200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:48135800-48140600	Weak transcription	HUVEC	blood vessel
22	chr12:48135800-48145400	Weak transcription	NHDF-Ad	bronchial
23	chr12:48136000-48139400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:48136000-48139600	Weak transcription	Primary B cells from cord blood	blood
25	chr12:48136000-48146200	Weak transcription	Osteobl	bone
26	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:48136400-48139000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:48136400-48140400	Weak transcription	Placenta	Placenta
29	chr12:48136600-48139400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:48136600-48140400	Weak transcription	Stomach Mucosa	stomach
31	chr12:48136600-48142400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:48137000-48139800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:48137200-48139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:48137400-48139800	Enhancers	Brain Hippocampus Middle	brain
35	chr12:48137400-48142000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:48137800-48139400	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:48137800-48139600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:48137800-48140000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:48137800-48145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:48138000-48139800	Weak transcription	Adipose Nuclei	Adipose
41	chr12:48138000-48140600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:48138000-48141000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:48138000-48144200	Weak transcription	Pancreas	Pancrea
44	chr12:48138000-48148000	Weak transcription	Liver	Liver
45	chr12:48138200-48140000	Enhancers	Brain Germinal Matrix	brain
46	chr12:48138400-48140000	Enhancers	Brain Substantia Nigra	brain
47	chr12:48138400-48140200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:48138400-48146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:48138600-48139000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:48138600-48139000	Enhancers	K562	blood

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