Variant report

Variant	rs62183783
Chromosome Location	chr2:172865775-172865776
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	ESR1	chr2:172865661-172865926	ECC-1	luminal epithelium:	n/a	n/a
2	TBL1XR1	chr2:172864349-172865814	K562	blood:	n/a	n/a
3	TEAD4	chr2:172864312-172865939	HepG2	liver:	n/a	n/a
4	IRF1	chr2:172864322-172866100	K562	blood:	n/a	n/a
5	MAZ	chr2:172864469-172865887	IMR90	lung:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
6	EP300	chr2:172864767-172866005	GM12878	blood:	n/a	chr2:172864819-172864835 chr2:172865374-172865388 chr2:172865065-172865072
7	MYC	chr2:172864443-172866003	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
8	MAX	chr2:172865641-172865973	K562	blood:	n/a	n/a
9	TBL1XR1	chr2:172864297-172865847	K562	blood:	n/a	n/a
10	POLR2A	chr2:172864483-172866178	K562	blood:	n/a	n/a
11	POLR2A	chr2:172864422-172866036	K562	blood:	n/a	n/a
12	MYC	chr2:172864384-172866113	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
13	ZNF384	chr2:172864695-172866150	K562	blood:	n/a	n/a
14	POLR2A	chr2:172864093-172865899	K562	blood:	n/a	n/a
15	POLR2A	chr2:172864490-172865854	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr2:172864384-172866232	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
17	MYC	chr2:172865687-172865880	NB4	blood:	n/a	n/a
18	MXI1	chr2:172863964-172866076	SK-N-SH	brain:	n/a	chr2:172865133-172865142
19	JUN	chr2:172864128-172866370	K562	blood:	n/a	chr2:172864832-172864841
20	MAX	chr2:172864419-172866140	NB4	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
21	TBP	chr2:172864332-172866122	K562	blood:	n/a	n/a
22	TAF1	chr2:172865639-172865989	K562	blood:	n/a	n/a
23	MYC	chr2:172864545-172865854	MCF10A-Er-Src	breast:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
24	MYC	chr2:172864469-172866119	K562	blood:	n/a	chr2:172865132-172865145 chr2:172865134-172865143 chr2:172865134-172865143 chr2:172865133-172865144 chr2:172865134-172865144 chr2:172865134-172865144 chr2:172865133-172865144 chr2:172865134-172865143 chr2:172865133-172865144
25	POLR2A	chr2:172864379-172866075	K562	blood:	n/a	n/a
26	POLR2A	chr2:172865632-172866105	K562	blood:	n/a	n/a
27	POLR2A	chr2:172865638-172865982	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172864878..172867088-chr2:172885343..172888601,3	MCF-7	breast:
2	chr2:172836942..172840182-chr2:172865086..172867545,3	K562	blood:
3	chr2:172863226..172865802-chr2:172966081..172969208,5	MCF-7	breast:
4	chr2:172865192..172866696-chr2:172882365..172884619,2	K562	blood:
5	chr2:172860607..172867322-chr2:172946572..172954768,24	MCF-7	breast:
6	chr2:172863189..172867097-chr2:172945137..172953576,15	K562	blood:
7	chr2:172777448..172780536-chr2:172864307..172867165,5	K562	blood:
8	chr2:172777448..172780686-chr2:172863264..172866650,5	K562	blood:
9	chr2:172859788..172868192-chr2:172944876..172951443,18	MCF-7	breast:
10	chr2:172861569..172867068-chr2:172965912..172971063,13	K562	blood:
11	chr2:172863189..172870519-chr2:172946500..172952655,22	K562	blood:
12	chr2:172865319..172867165-chr2:172958797..172961537,3	MCF-7	breast:
13	chr2:172289221..172292184-chr2:172864925..172866500,2	K562	blood:
14	chr2:172377500..172380432-chr2:172864656..172866178,2	K562	blood:
15	chr2:172837275..172840182-chr2:172865086..172867056,2	K562	blood:
16	chr2:172749212..172752099-chr2:172863500..172865923,3	MCF-7	breast:
17	chr11:65265208..65268065-chr2:172864519..172866349,2	MCF-7	breast:
18	chr2:172862808..172868920-chr2:172961807..172971063,13	K562	blood:
19	chr2:85843078..85843730-chr2:172865077..172865933,2	Hela-S3	cervix:

Variant related genes	Relation type
SLC25A12	TF binding region
ENSG00000115827	Chromatin interaction
ENSG00000071967	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000172878	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000128708	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs55653103	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62183782	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183784	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183785	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183800	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183801	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6718013	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729945	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6730085	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733794	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6746701	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7557612	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584187	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598246	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62183783	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs62183783	AC068039.4	cis	Esophagus Muscularis	GTEx
rs62183783	AC068039.4	cis	Thyroid	GTEx
rs62183783	AC068039.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172864000-172865800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:172864000-172865800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr2:172864000-172865800	Active TSS	A549	lung
4	chr2:172864200-172866000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:172864400-172865800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:172864400-172865800	Active TSS	Fetal Stomach	stomach
7	chr2:172864400-172865800	Active TSS	K562	blood
8	chr2:172864400-172865800	Active TSS	NHLF	lung
9	chr2:172864400-172866200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:172864600-172865800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:172864600-172866000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:172864600-172866000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:172864600-172866000	Active TSS	HSMM	muscle
14	chr2:172865000-172865800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:172865000-172865800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr2:172865000-172865800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:172865000-172866000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr2:172865000-172866000	Flanking Active TSS	GM12878-XiMat	blood
19	chr2:172865000-172866200	Flanking Active TSS	Dnd41	blood
20	chr2:172865200-172865800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:172865200-172865800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:172865200-172865800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr2:172865200-172865800	Flanking Active TSS	Hela-S3	cervix
24	chr2:172865200-172865800	Flanking Active TSS	NH-A	brain
25	chr2:172865200-172865800	Flanking Active TSS	NHEK	skin
26	chr2:172865200-172865800	Flanking Active TSS	Osteobl	bone
27	chr2:172865200-172866000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:172865400-172865800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:172865400-172865800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:172865400-172865800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:172865400-172865800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:172865400-172865800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:172865400-172865800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:172865400-172865800	Enhancers	Primary B cells from cord blood	blood
36	chr2:172865400-172865800	Enhancers	Primary B cells from peripheral blood	blood
37	chr2:172865400-172865800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:172865400-172865800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:172865400-172865800	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:172865400-172865800	Enhancers	Colonic Mucosa	Colon
41	chr2:172865400-172866000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:172865400-172866000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:172865400-172866000	Enhancers	Fetal Thymus	thymus
44	chr2:172865400-172866000	Flanking Active TSS	HepG2	liver
45	chr2:172865400-172877200	Weak transcription	Pancreas	Pancrea
46	chr2:172865400-172878000	Weak transcription	Gastric	stomach
47	chr2:172865600-172865800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr2:172865600-172865800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:172865600-172865800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:172865600-172865800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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