Variant report

Variant	rs28458281
Chromosome Location	chr3:179139279-179139280
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:179139255-179139786	MCF-7	breast:	n/a	n/a
2	RAD21	chr3:179139270-179139781	ECC-1	luminal epithelium:	n/a	n/a
3	RAD21	chr3:179139244-179139879	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr3:179139256-179139742	T-47D	breast:	n/a	n/a
5	SMC3	chr3:179139248-179139856	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr3:179139151-179139845	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr3:179139252-179139767	A549	lung:	n/a	n/a
8	CTCF	chr3:179139260-179139744	HCT-116	colon:	n/a	n/a
9	RAD21	chr3:179139259-179139801	MCF-7	breast:	n/a	n/a
10	RAD21	chr3:179139241-179139748	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	chr3:179133727..179135378-chr3:179139068..179141820,2	K562	blood:
2	chr3:179138994..179139550-chr3:179276259..179276771,2	K562	blood:
3	chr3:179138990..179139711-chr3:179276330..179277153,2	MCF-7	breast:
4	chr3:179138968..179140051-chr3:179276271..179277260,8	MCF-7	breast:

No data

Variant related genes	Relation type
GNB4	TF binding region
ENSG00000114450	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2287212	0.86[AFR][1000 genomes]
rs28525971	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56231352	1.00[ASN][1000 genomes]
rs58167439	1.00[ASN][1000 genomes]
rs60118786	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61735185	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768421	1.00[ASN][1000 genomes]
rs6769014	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792924	1.00[ASN][1000 genomes]
rs73043415	1.00[ASN][1000 genomes]
rs9877546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877945	1.00[ASN][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
2	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
5	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
8	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
9	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
10	chr3:179112200-179142600	Weak transcription	Esophagus	oesophagus
11	chr3:179112800-179144200	Weak transcription	A549	lung
12	chr3:179113800-179146800	Weak transcription	Gastric	stomach
13	chr3:179115600-179139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:179120600-179143800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:179120800-179144600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:179121000-179139400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:179121000-179149400	Weak transcription	Primary T cells from cord blood	blood
18	chr3:179121400-179143000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:179122400-179142000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:179122800-179149800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:179123000-179143000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:179123000-179143200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:179123000-179150400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:179123200-179141000	Weak transcription	K562	blood
25	chr3:179123200-179141800	Weak transcription	Aorta	Aorta
26	chr3:179123200-179142200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:179123200-179154800	Weak transcription	Brain Anterior Caudate	brain
28	chr3:179123400-179141000	Weak transcription	Brain Germinal Matrix	brain
29	chr3:179123400-179142400	Weak transcription	Right Ventricle	heart
30	chr3:179123400-179149600	Weak transcription	Fetal Intestine Large	intestine
31	chr3:179123600-179153600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:179123800-179156400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:179124000-179141000	Weak transcription	Liver	Liver
34	chr3:179124200-179141000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:179125600-179141000	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:179125600-179141800	Weak transcription	Ovary	ovary
37	chr3:179125600-179142000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:179127200-179145000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:179127600-179145200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr3:179131000-179141000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:179131000-179141800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:179131400-179141000	Weak transcription	Spleen	Spleen
43	chr3:179131600-179141000	Weak transcription	Lung	lung
44	chr3:179131600-179147400	Weak transcription	Fetal Heart	heart
45	chr3:179132600-179141600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:179132800-179141000	Weak transcription	NHEK	skin
47	chr3:179132800-179167000	Weak transcription	Hela-S3	cervix
48	chr3:179133000-179142600	Weak transcription	HMEC	breast
49	chr3:179133200-179149400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:179133400-179150400	Weak transcription	Brain Cingulate Gyrus	brain

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