Variant report

Variant	rs12489192
Chromosome Location	chr3:113463385-113463386
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr3:113463284-113467309	IMR90	lung:	n/a	n/a
2	ZNF384	chr3:113463168-113463429	K562	blood:	n/a	n/a
3	CHD1	chr3:113463300-113464852	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:113449273..113452102-chr3:113460685..113464475,4	K562	blood:
2	chr3:113454872..113455949-chr3:113463185..113464560,4	MCF-7	breast:
3	chr3:113411906..113415827-chr3:113462156..113465985,7	MCF-7	breast:
4	chr3:113412999..113415716-chr3:113462396..113464143,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239280	TF binding region
ATP6V1A	TF binding region
NAA50	TF binding region
ENSG00000176542	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10934239	0.87[AMR][1000 genomes]
rs10934240	0.87[AMR][1000 genomes]
rs11920913	0.87[AMR][1000 genomes]
rs12486414	1.00[AMR][1000 genomes]
rs12490048	0.93[AMR][1000 genomes]
rs12490651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12491540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12492290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12492542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12492783	0.93[AMR][1000 genomes]
rs12493602	1.00[AMR][1000 genomes]
rs12493935	0.87[AMR][1000 genomes]
rs12494777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12495298	0.93[AMR][1000 genomes]
rs12495713	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12496604	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12496617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12497754	1.00[AMR][1000 genomes]
rs16861230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861233	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861235	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16861331	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2292512	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2566972	0.87[AMR][1000 genomes]
rs2603791	0.87[AMR][1000 genomes]
rs3773686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv1799124	chr3:113426201-113468350	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv482804	chr3:113432431-113581672	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
5	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 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	chr3:113437200-113464000	Weak transcription	Lung	lung
2	chr3:113440800-113463600	Weak transcription	Ovary	ovary
3	chr3:113442200-113463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:113453600-113463600	Enhancers	Liver	Liver
5	chr3:113456800-113463600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:113459600-113463600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:113459600-113463600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:113459800-113463800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:113460000-113465600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:113460200-113463400	Enhancers	Primary T cells from cord blood	blood
11	chr3:113460200-113463600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr3:113460400-113463800	Weak transcription	Aorta	Aorta
13	chr3:113461600-113463600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:113461600-113463600	Flanking Active TSS	NHEK	skin
15	chr3:113461800-113463400	Enhancers	Colon Smooth Muscle	Colon
16	chr3:113461800-113463400	Enhancers	Fetal Heart	heart
17	chr3:113461800-113463400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:113461800-113463400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr3:113461800-113463400	Flanking Active TSS	Osteobl	bone
20	chr3:113461800-113463600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:113461800-113463600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:113461800-113463600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:113461800-113463600	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:113461800-113463800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:113461800-113468400	Active TSS	K562	blood
26	chr3:113462000-113463600	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:113462000-113463600	Flanking Active TSS	HUVEC	blood vessel
28	chr3:113462200-113463400	Enhancers	Small Intestine	intestine
29	chr3:113462200-113463400	Flanking Active TSS	HMEC	breast
30	chr3:113462200-113463600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:113462200-113463600	Enhancers	Thymus	Thymus
32	chr3:113462200-113463800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:113462200-113463800	Flanking Active TSS	Hela-S3	cervix
34	chr3:113462200-113466800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:113462200-113467200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:113462400-113463600	Enhancers	Brain Hippocampus Middle	brain
37	chr3:113462400-113467200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr3:113462600-113463400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:113462600-113463400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:113462600-113463400	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:113462600-113463400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:113462600-113463400	Enhancers	Brain Anterior Caudate	brain
43	chr3:113462600-113463400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:113462600-113463600	Enhancers	Brain Cingulate Gyrus	brain
45	chr3:113462600-113463600	Enhancers	Brain Substantia Nigra	brain
46	chr3:113462600-113463600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:113462600-113463800	Enhancers	Stomach Mucosa	stomach
48	chr3:113462600-113466800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr3:113462800-113463400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:113462800-113463400	Enhancers	Fetal Brain Male	brain

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