Variant report

Variant	rs12490651
Chromosome Location	chr3:113470136-113470137
allele	A/C
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	STAT3	chr3:113469770-113470502	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:113469992-113470408	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:113470083-113470267	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr3:113470047-113470358	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:113470014-113470330	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr3:113470052-113470320	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr3:113469987-113470403	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr3:113470022-113470404	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:113470004-113470387	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113465419..113468176-chr3:113469348..113473059,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242659	TF binding region
NAA50	TF binding region
ENSG00000114573	Chromatin interaction
ENSG00000242659	Chromatin interaction

Extended variants
information (count: 32 )
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]
rs12489192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490048	0.93[AMR][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:6 , 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	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
4	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
5	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
6	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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113466800-113489000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:113467000-113472000	Weak transcription	Brain Germinal Matrix	brain
3	chr3:113467000-113473000	Weak transcription	Psoas Muscle	Psoas
4	chr3:113467200-113471800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:113467200-113471800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:113467200-113504000	Weak transcription	Fetal Stomach	stomach
7	chr3:113467200-113514800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:113467200-113528600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:113467400-113471600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:113467600-113488400	Weak transcription	NH-A	brain
11	chr3:113467800-113471600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:113467800-113473200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:113467800-113477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:113468000-113470600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:113468000-113470800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:113468000-113471200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:113468000-113471800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:113468000-113471800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:113468000-113472000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:113468000-113472000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:113468000-113477200	Weak transcription	Primary T cells from cord blood	blood
22	chr3:113468000-113477200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:113468000-113487800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:113468000-113488200	Weak transcription	A549	lung
25	chr3:113468000-113488600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:113468000-113495200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:113468000-113499800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:113468000-113502800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:113468200-113472000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:113468200-113472600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:113468200-113473000	Weak transcription	HUVEC	blood vessel
32	chr3:113468200-113473200	Weak transcription	Right Atrium	heart
33	chr3:113468200-113476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:113468200-113488400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:113468400-113472000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:113468600-113471800	Weak transcription	HMEC	breast
37	chr3:113468600-113472000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:113468600-113472200	Weak transcription	Brain Anterior Caudate	brain
39	chr3:113468600-113472200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:113468600-113472600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:113468600-113476000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:113468600-113488400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:113468800-113471800	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:113468800-113472200	Weak transcription	Brain Angular Gyrus	brain
45	chr3:113468800-113473400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:113468800-113477400	Weak transcription	Liver	Liver
47	chr3:113469000-113471800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:113469000-113472000	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:113469000-113472800	Weak transcription	Primary B cells from cord blood	blood
50	chr3:113469000-113473000	Weak transcription	GM12878-XiMat	blood

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