Variant report

Variant	rs12239445
Chromosome Location	chr1:223938836-223938837
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	FOXA1	chr1:223938800-223939341	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:223938829-223938862	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:223938821-223940662	U87	brain:	n/a	n/a
4	MAX	chr1:223938695-223939281	HepG2	liver:	n/a	chr1:223938798-223938809 chr1:223938797-223938810 chr1:223938798-223938808 chr1:223938798-223938808
5	POLR2A	chr1:223938463-223939342	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:223937857-223950461	K562	blood:	n/a	n/a
7	HNF4A	chr1:223938812-223939248	HepG2	liver:	n/a	chr1:223939027-223939042 chr1:223939029-223939041 chr1:223939029-223939041 chr1:223939027-223939042 chr1:223939027-223939042 chr1:223939027-223939042 chr1:223939029-223939041 chr1:223939028-223939041 chr1:223939029-223939042 chr1:223939027-223939042 chr1:223939028-223939040 chr1:223939028-223939042 chr1:223939026-223939044 chr1:223939028-223939042
8	POLR2A	chr1:223938018-223939146	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223936854..223938919-chr1:223960180..223962303,2	K562	blood:
2	chr1:223937050..223939736-chr1:223946719..223949161,2	K562	blood:
3	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:
4	chr1:223936472..223939236-chr1:224031329..224033727,2	K562	blood:
5	chr1:223915826..223918177-chr1:223937169..223939533,2	K562	blood:
6	chr1:223898965..223904523-chr1:223935616..223939096,7	MCF-7	breast:

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000162909	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158199	1.00[EUR][1000 genomes]
rs10158508	1.00[EUR][1000 genomes]
rs10158843	1.00[EUR][1000 genomes]
rs10159010	1.00[EUR][1000 genomes]
rs1153962	1.00[EUR][1000 genomes]
rs1153966	1.00[EUR][1000 genomes]
rs12025911	1.00[EUR][1000 genomes]
rs12026548	1.00[EUR][1000 genomes]
rs12027762	1.00[EUR][1000 genomes]
rs12040996	1.00[EUR][1000 genomes]
rs12047952	1.00[EUR][1000 genomes]
rs1222131	1.00[EUR][1000 genomes]
rs12239402	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12239678	1.00[EUR][1000 genomes]
rs13375296	1.00[EUR][1000 genomes]
rs16842078	1.00[EUR][1000 genomes]
rs16842173	1.00[EUR][1000 genomes]
rs16842177	1.00[EUR][1000 genomes]
rs16842201	1.00[EUR][1000 genomes]
rs16842217	1.00[EUR][1000 genomes]
rs16842234	1.00[EUR][1000 genomes]
rs16842259	1.00[EUR][1000 genomes]
rs16842291	1.00[EUR][1000 genomes]
rs16842341	1.00[EUR][1000 genomes]
rs1890119	1.00[EUR][1000 genomes]
rs2230082	1.00[EUR][1000 genomes]
rs28370064	1.00[EUR][1000 genomes]
rs28370079	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28370099	1.00[EUR][1000 genomes]
rs28370160	1.00[EUR][1000 genomes]
rs28370161	1.00[EUR][1000 genomes]
rs28370162	1.00[EUR][1000 genomes]
rs28458390	1.00[EUR][1000 genomes]
rs28684725	1.00[EUR][1000 genomes]
rs41345146	1.00[EUR][1000 genomes]
rs56947789	1.00[EUR][1000 genomes]
rs57380389	1.00[EUR][1000 genomes]
rs58753599	1.00[EUR][1000 genomes]
rs59433589	1.00[EUR][1000 genomes]
rs59793743	1.00[EUR][1000 genomes]
rs59948383	1.00[EUR][1000 genomes]
rs59970447	1.00[EUR][1000 genomes]
rs73114413	1.00[EUR][1000 genomes]
rs73125398	1.00[EUR][1000 genomes]
rs73127405	1.00[EUR][1000 genomes]
rs73127411	1.00[EUR][1000 genomes]
rs73127438	1.00[EUR][1000 genomes]
rs73127450	1.00[EUR][1000 genomes]
rs747811	1.00[EUR][1000 genomes]
rs7515215	1.00[EUR][1000 genomes]
rs9286986	1.00[EUR][1000 genomes]
rs9970756	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:223936800-223947400	Weak transcription	Fetal Brain Male	brain
7	chr1:223936800-223954400	Strong transcription	HSMM	muscle
8	chr1:223937000-223939000	Weak transcription	Liver	Liver
9	chr1:223937000-223939000	Weak transcription	Fetal Thymus	thymus
10	chr1:223937000-223939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:223937000-223939600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:223937000-223940000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:223937000-223940200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:223937000-223940200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:223937000-223940200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:223937000-223940200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:223937000-223940200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:223937000-223940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:223937000-223940400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:223937000-223940600	Weak transcription	Small Intestine	intestine
21	chr1:223937000-223940800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:223937000-223943200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:223937000-223943400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr1:223937000-223945400	Strong transcription	Hela-S3	cervix
25	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:223937000-223948000	Strong transcription	Lung	lung
27	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
28	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:223937000-223954400	Strong transcription	Colonic Mucosa	Colon
30	chr1:223937000-223954400	Strong transcription	Esophagus	oesophagus
31	chr1:223937000-223954400	Strong transcription	Gastric	stomach
32	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
37	chr1:223937000-223954800	Strong transcription	Osteobl	bone
38	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
41	chr1:223937200-223940200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:223937200-223940200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:223937200-223940400	Weak transcription	Primary B cells from cord blood	blood
44	chr1:223937200-223940600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:223937200-223942400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:223937200-223943000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:223937200-223948600	Strong transcription	HUVEC	blood vessel
48	chr1:223937200-223951800	Strong transcription	HSMMtube	muscle
49	chr1:223937200-223952600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:223937200-223953000	Strong transcription	Skeletal Muscle Male	skeletal muscle

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