Variant report

Variant	rs12064322
Chromosome Location	chr1:228673718-228673719
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	RFX5	chr1:228673704-228675743	IMR90	lung:	n/a	chr1:228674183-228674198
2	POLR2A	chr1:228673607-228673852	HCT-116	colon:	n/a	n/a
3	E2F6	chr1:228673619-228673777	K562	blood:	n/a	n/a
4	POLR2A	chr1:228673510-228673740	HepG2	liver:	n/a	n/a
5	MYC	chr1:228673552-228673897	K562	blood:	n/a	n/a
6	CEBPB	chr1:228673646-228673960	K562	blood:	n/a	chr1:228673806-228673817 chr1:228673804-228673817
7	JUN	chr1:228672601-228678958	K562	blood:	n/a	chr1:228677697-228677705 chr1:228678292-228678303

No.	Distal block	Cell Line	Cell type
1	chr1:11967567..11969704-chr1:228673208..228675906,2	MCF-7	breast:
2	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:
3	chr1:228671614..228676496-chr1:228676543..228681096,6	MCF-7	breast:
4	chr1:228672968..228678350-chr1:228679226..228685848,20	MCF-7	breast:
5	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:
6	chr1:228673229..228674751-chr9:33024497..33026836,2	MCF-7	breast:
7	chr1:228321585..228323850-chr1:228673376..228675624,2	K562	blood:

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000137074	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000227625	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000086061	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10916309	1.00[EUR][1000 genomes]
rs10916310	1.00[EUR][1000 genomes]
rs10916312	1.00[EUR][1000 genomes]
rs10916345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804099	1.00[EUR][1000 genomes]
rs11808955	1.00[EUR][1000 genomes]
rs1188486	1.00[EUR][1000 genomes]
rs12057947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066800	1.00[EUR][1000 genomes]
rs12073379	1.00[EUR][1000 genomes]
rs12074377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084050	1.00[EUR][1000 genomes]
rs12095133	1.00[EUR][1000 genomes]
rs12095950	1.00[EUR][1000 genomes]
rs16848604	1.00[EUR][1000 genomes]
rs16848741	1.00[EUR][1000 genomes]
rs2087120	1.00[EUR][1000 genomes]
rs34087163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs473316	1.00[EUR][1000 genomes]
rs477699	1.00[EUR][1000 genomes]
rs56690462	1.00[EUR][1000 genomes]
rs56757399	1.00[EUR][1000 genomes]
rs58560450	1.00[EUR][1000 genomes]
rs58670384	1.00[EUR][1000 genomes]
rs59958468	1.00[EUR][1000 genomes]
rs61149796	1.00[EUR][1000 genomes]
rs61416971	1.00[EUR][1000 genomes]
rs6692594	1.00[EUR][1000 genomes]
rs73099694	1.00[EUR][1000 genomes]
rs73101117	1.00[EUR][1000 genomes]
rs74144509	1.00[EUR][1000 genomes]
rs7513176	1.00[EUR][1000 genomes]
rs7514849	1.00[EUR][1000 genomes]
rs827827	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
12	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
13	esv3417507	chr1:228673529-228677127	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr1:228667400-228674000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:228667600-228673800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:228667600-228674000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:228667800-228673800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:228667800-228674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228668000-228674000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:228668200-228673800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:228670800-228673800	Weak transcription	GM12878-XiMat	blood
9	chr1:228672000-228673800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:228672200-228673800	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:228672600-228673800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:228672800-228673800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:228672800-228673800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr1:228672800-228674000	Enhancers	HUVEC	blood vessel
15	chr1:228673000-228673800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:228673000-228673800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:228673000-228673800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:228673000-228674000	Enhancers	Liver	Liver
19	chr1:228673000-228674000	Enhancers	NHDF-Ad	bronchial
20	chr1:228673200-228673800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:228673200-228673800	Enhancers	NHLF	lung
22	chr1:228673200-228673800	Enhancers	Osteobl	bone
23	chr1:228673200-228674000	Enhancers	Fetal Lung	lung
24	chr1:228673400-228673800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:228673400-228673800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:228673400-228673800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:228673400-228673800	Enhancers	HepG2	liver
28	chr1:228673400-228673800	Weak transcription	HMEC	breast
29	chr1:228673400-228674000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:228673400-228674000	Enhancers	Adipose Nuclei	Adipose
31	chr1:228673400-228674000	Weak transcription	Stomach Mucosa	stomach
32	chr1:228673600-228673800	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:228673600-228673800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:228673600-228673800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:228673600-228673800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:228673600-228673800	Enhancers	Brain Hippocampus Middle	brain
37	chr1:228673600-228673800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:228673600-228673800	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:228673600-228673800	Enhancers	Fetal Muscle Leg	muscle
40	chr1:228673600-228673800	Enhancers	Fetal Stomach	stomach
41	chr1:228673600-228673800	Enhancers	Fetal Thymus	thymus
42	chr1:228673600-228673800	Enhancers	Psoas Muscle	Psoas
43	chr1:228673600-228673800	Enhancers	Right Atrium	heart
44	chr1:228673600-228673800	Flanking Active TSS	Dnd41	blood
45	chr1:228673600-228673800	Weak transcription	NHEK	skin
46	chr1:228673600-228674000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:228673600-228674000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:228673600-228674000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr1:228673600-228674000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:228673600-228674000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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