Variant report

Variant	rs9877546
Chromosome Location	chr3:179137102-179137103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179136011..179138741-chr3:179276797..179278393,2	MCF-7	breast:
2	chr3:179135593..179139042-chr3:179279832..179281537,3	K562	blood:

Variant related genes	Relation type
ENSG00000136518	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2287212	0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs28458281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792924	1.00[ASN][1000 genomes]
rs6807219	0.81[YRI][hapmap]
rs73043415	1.00[ASN][1000 genomes]
rs7617958	0.81[YRI][hapmap]
rs7639279	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9872894	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9877945	1.00[CHB][hapmap];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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
2	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
3	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:179096600-179142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:179097000-179147400	Weak transcription	Small Intestine	intestine
6	chr3:179102200-179144400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:179105200-179144600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:179105400-179141400	Weak transcription	Thymus	Thymus
9	chr3:179111600-179138600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:179111800-179150600	Weak transcription	Psoas Muscle	Psoas
11	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
12	chr3:179112200-179138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:179112200-179142600	Weak transcription	Esophagus	oesophagus
14	chr3:179112800-179144200	Weak transcription	A549	lung
15	chr3:179113800-179146800	Weak transcription	Gastric	stomach
16	chr3:179114200-179139200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:179115600-179139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:179118000-179137600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:179120600-179138000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:179120600-179143800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:179120800-179144600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:179121000-179139400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:179121000-179149400	Weak transcription	Primary T cells from cord blood	blood
24	chr3:179121400-179143000	Weak transcription	Fetal Intestine Small	intestine
25	chr3:179122400-179142000	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:179122600-179138200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:179122800-179149800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:179123000-179143000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:179123000-179143200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:179123000-179150400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:179123200-179141000	Weak transcription	K562	blood
32	chr3:179123200-179141800	Weak transcription	Aorta	Aorta
33	chr3:179123200-179142200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:179123200-179154800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:179123400-179141000	Weak transcription	Brain Germinal Matrix	brain
36	chr3:179123400-179142400	Weak transcription	Right Ventricle	heart
37	chr3:179123400-179149600	Weak transcription	Fetal Intestine Large	intestine
38	chr3:179123600-179153600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:179123800-179156400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:179124000-179141000	Weak transcription	Liver	Liver
41	chr3:179124200-179141000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:179125600-179141000	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:179125600-179141800	Weak transcription	Ovary	ovary
44	chr3:179125600-179142000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:179127200-179145000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:179127600-179137400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:179127600-179137400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:179127600-179145200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:179127800-179137400	Strong transcription	Dnd41	blood
50	chr3:179128800-179138400	Strong transcription	Primary monocytes fromperipheralblood	blood

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