Variant report

Variant	rs58174591
Chromosome Location	chr3:120044872-120044873
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	chr3:120044381..120045937-chr3:120067241..120069231,2	MCF-7	breast:
2	chr3:120044201..120047404-chr3:120067957..120069796,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR156-1	chr3:120044178-120047197	NONHSAT091437

Variant related genes	Relation type
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs41271405	1.00[EUR][1000 genomes]
rs55640624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55885326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048284	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56239327	1.00[EUR][1000 genomes]
rs56281929	1.00[EUR][1000 genomes]
rs56384860	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58296615	1.00[EUR][1000 genomes]
rs58932850	1.00[EUR][1000 genomes]
rs59522791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59766787	1.00[EUR][1000 genomes]
rs59779647	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60136263	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60814807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61160321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61535593	1.00[EUR][1000 genomes]
rs6764372	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956853	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72956897	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958712	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958714	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72958778	1.00[EUR][1000 genomes]
rs73855206	1.00[EUR][1000 genomes]
rs73855223	1.00[EUR][1000 genomes]
rs73855241	1.00[EUR][1000 genomes]
rs73856465	1.00[EUR][1000 genomes]
rs73856468	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
5	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:120033200-120050000	Weak transcription	Spleen	Spleen
8	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
10	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:120034600-120052400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:120035200-120049800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:120036600-120053600	Weak transcription	Fetal Heart	heart
14	chr3:120037200-120052200	Weak transcription	Brain Anterior Caudate	brain
15	chr3:120038200-120049200	Weak transcription	Fetal Kidney	kidney
16	chr3:120038400-120046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:120038600-120049200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:120038800-120049000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:120038800-120049800	Weak transcription	Fetal Brain Female	brain
20	chr3:120038800-120051600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:120039000-120046600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:120039000-120048000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:120039200-120053600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:120039400-120046600	Weak transcription	Left Ventricle	heart
25	chr3:120039600-120046800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:120039600-120049400	Weak transcription	NHLF	lung
27	chr3:120039800-120049400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:120040000-120046600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:120040000-120049000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:120040200-120048400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:120040200-120049000	Weak transcription	HUVEC	blood vessel
32	chr3:120040200-120049200	Weak transcription	Hela-S3	cervix
33	chr3:120040400-120045800	Weak transcription	Primary B cells from cord blood	blood
34	chr3:120040400-120049000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:120040400-120049800	Weak transcription	Brain Angular Gyrus	brain
36	chr3:120040400-120055000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:120040400-120056400	Strong transcription	Dnd41	blood
38	chr3:120041000-120046600	Weak transcription	Liver	Liver
39	chr3:120041000-120046600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:120041000-120049000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:120041000-120049200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:120041000-120049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:120041000-120056200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:120041000-120057400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:120041000-120057400	Weak transcription	Small Intestine	intestine
46	chr3:120041000-120058000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:120041200-120045000	Strong transcription	Fetal Thymus	thymus
48	chr3:120041200-120048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:120041200-120049000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:120041200-120049200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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