Variant report

Variant	rs12034519
Chromosome Location	chr1:228676824-228676825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228675488-228676933	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:228675579-228678949	K562	blood:	n/a	n/a
3	POLR2A	chr1:228675691-228676901	U87	brain:	n/a	n/a
4	POLR2A	chr1:228674145-228676899	K562	blood:	n/a	n/a
5	POLR2A	chr1:228676148-228676865	K562	blood:	n/a	n/a
6	POLR2A	chr1:228676512-228676832	ProgFib	skin:	n/a	n/a
7	POLR2A	chr1:228674162-228676850	GM12878	blood:	n/a	n/a
8	MXI1	chr1:228673999-228676881	IMR90	lung:	n/a	n/a
9	POLR2A	chr1:228673803-228676876	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:228675567-228676947	U87	brain:	n/a	n/a
11	POLR2A	chr1:228676435-228676963	U87	brain:	n/a	n/a
12	POLR2A	chr1:228675568-228676966	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr1:228674188-228676862	GM15510	blood:	n/a	n/a
14	POLR2A	chr1:228676183-228676897	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr1:228675820-228677245	PBDE	blood:	n/a	n/a
16	MAZ	chr1:228674170-228676873	K562	blood:	n/a	chr1:228675761-228675771
17	POLR2A	chr1:228674245-228676862	K562	blood:	n/a	n/a
18	POLR2A	chr1:228673999-228676834	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr1:228674156-228676916	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:228674075-228677148	Raji	blood:	n/a	n/a
21	POLR2A	chr1:228676789-228676859	Hela-S3	cervix:	n/a	n/a
22	JUN	chr1:228672601-228678958	K562	blood:	n/a	chr1:228677697-228677705 chr1:228678292-228678303

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228400032..228401961-chr1:228675104..228677391,2	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	chr1:228675436..228678007-chr1:228697619..228700594,3	MCF-7	breast:
5	chr1:228672968..228678350-chr1:228679226..228685848,20	MCF-7	breast:
6	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:

No data

Variant related genes	Relation type
RNF187	TF binding region
ENSG00000215811	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000162913	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12035875	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12407568	1.00[EUR][1000 genomes]
rs4653977	1.00[EUR][1000 genomes]
rs4653979	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	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
11	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
12	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
13	esv3338881	chr1:228674354-228676902	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228675400-228684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:228675600-228677400	Enhancers	Fetal Brain Male	brain
3	chr1:228675800-228677000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr1:228675800-228677000	Flanking Active TSS	Brain Hippocampus Middle	brain
5	chr1:228676000-228677000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:228676000-228677000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
7	chr1:228676000-228677000	Flanking Active TSS	Fetal Brain Female	brain
8	chr1:228676000-228677200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:228676000-228677200	Flanking Active TSS	HepG2	liver
10	chr1:228676000-228678800	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr1:228676200-228677000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:228676200-228677000	Enhancers	Primary B cells from cord blood	blood
13	chr1:228676200-228677000	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:228676200-228677000	Weak transcription	Fetal Kidney	kidney
15	chr1:228676200-228677200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:228676200-228677200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:228676200-228677400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:228676200-228678000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:228676400-228677000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:228676400-228677000	Enhancers	Brain Angular Gyrus	brain
21	chr1:228676400-228677000	Genic enhancers	Fetal Stomach	stomach
22	chr1:228676400-228677000	Genic enhancers	Fetal Thymus	thymus
23	chr1:228676400-228677000	Enhancers	Lung	lung
24	chr1:228676400-228677000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
25	chr1:228676400-228677200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:228676400-228677200	Enhancers	Brain Substantia Nigra	brain
27	chr1:228676400-228677200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
28	chr1:228676400-228677400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:228676400-228677400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:228676400-228677600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:228676400-228677600	Enhancers	Colonic Mucosa	Colon
32	chr1:228676400-228677800	Weak transcription	Aorta	Aorta
33	chr1:228676400-228677800	Enhancers	Right Ventricle	heart
34	chr1:228676400-228678000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:228676400-228678000	Enhancers	Left Ventricle	heart
36	chr1:228676400-228678800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:228676400-228683000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:228676400-228684800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:228676400-228685200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:228676400-228688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:228676600-228677000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:228676600-228677000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:228676600-228677000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:228676600-228677000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:228676600-228677000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:228676600-228677000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:228676600-228677000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:228676600-228677000	Enhancers	Osteobl	bone
49	chr1:228676600-228677200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr1:228676600-228677200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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