Variant report

Variant	rs58509367
Chromosome Location	chr2:47006008-47006009
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47005678..47008315-chr2:47011541..47013639,2	MCF-7	breast:
2	chr2:46872190..46873901-chr2:47005919..47008590,2	K562	blood:
3	chr2:46881672..46884638-chr2:47005149..47007963,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SOCS5-1	chr2:47004922-47007384	ENSG00000260977.1

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10495937	1.00[ASN][1000 genomes]
rs1446496	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446497	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446498	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035524	1.00[ASN][1000 genomes]
rs17771098	1.00[ASN][1000 genomes]
rs17771201	1.00[ASN][1000 genomes]
rs17771942	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17772285	0.86[AMR][1000 genomes]
rs17773016	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821989	0.86[AMR][1000 genomes]
rs17822782	0.86[AMR][1000 genomes]
rs17823065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045290	0.86[AMR][1000 genomes]
rs41453849	0.83[ASN][1000 genomes]
rs41489952	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55928499	1.00[ASN][1000 genomes]
rs56060227	0.83[ASN][1000 genomes]
rs56199036	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56800355	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57124017	1.00[ASN][1000 genomes]
rs57420323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58200475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58362257	0.83[ASN][1000 genomes]
rs58903656	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59186028	1.00[ASN][1000 genomes]
rs59785662	1.00[ASN][1000 genomes]
rs59882453	0.83[ASN][1000 genomes]
rs60506146	1.00[ASN][1000 genomes]
rs61075718	0.83[ASN][1000 genomes]
rs61654472	0.83[ASN][1000 genomes]
rs72802420	0.86[AMR][1000 genomes]
rs72802426	0.86[AMR][1000 genomes]
rs72802441	1.00[ASN][1000 genomes]
rs72802445	1.00[ASN][1000 genomes]
rs72802448	0.86[AMR][1000 genomes]
rs72802451	0.86[AMR][1000 genomes]
rs72802454	0.86[AMR][1000 genomes]
rs72802455	0.86[AMR][1000 genomes]
rs72802456	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802458	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802463	1.00[ASN][1000 genomes]
rs72802464	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802465	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802466	0.86[AMR][1000 genomes]
rs72802467	0.86[AMR][1000 genomes]
rs72802468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72802469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72802470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72802486	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802487	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802492	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802493	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802498	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72802499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72804404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72804430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7566275	1.00[ASN][1000 genomes]
rs7578911	1.00[ASN][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	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats 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 target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv213378	chr2:47001834-47006121	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46981400-47006800	Weak transcription	Psoas Muscle	Psoas
2	chr2:46985600-47008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:47001000-47008600	Enhancers	Osteobl	bone
4	chr2:47002800-47007000	Weak transcription	Ovary	ovary
5	chr2:47004000-47006200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:47004000-47006600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:47005000-47006400	Enhancers	A549	lung
8	chr2:47005000-47008600	Enhancers	HepG2	liver
9	chr2:47005200-47009400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47005200-47010000	Enhancers	Fetal Lung	lung
11	chr2:47005400-47006200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:47005400-47009200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:47005400-47009200	Enhancers	NHLF	lung
14	chr2:47005400-47009400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:47005400-47012400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:47005600-47006200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:47005600-47006200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:47005600-47006200	Enhancers	Fetal Brain Male	brain
19	chr2:47005600-47006200	Enhancers	Right Atrium	heart
20	chr2:47005600-47006400	Weak transcription	Fetal Stomach	stomach
21	chr2:47005600-47006400	Weak transcription	Right Ventricle	heart
22	chr2:47005600-47007000	Enhancers	NHEK	skin
23	chr2:47005600-47008200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:47005600-47008200	Enhancers	HMEC	breast
25	chr2:47005600-47009400	Enhancers	Fetal Heart	heart
26	chr2:47005600-47009400	Enhancers	NHDF-Ad	bronchial
27	chr2:47005600-47010000	Enhancers	Left Ventricle	heart
28	chr2:47005800-47006400	Weak transcription	Stomach Mucosa	stomach
29	chr2:47005800-47006600	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:47005800-47007400	Enhancers	Hela-S3	cervix
31	chr2:47005800-47008200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:47005800-47008200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:47005800-47008400	Enhancers	NH-A	brain
34	chr2:47005800-47009000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:47005800-47009200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:47005800-47009800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr2:47006000-47006600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:47006000-47006600	Weak transcription	Lung	lung
39	chr2:47006000-47006800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:47006000-47007200	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:47006000-47007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:47006000-47008200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:47006000-47008400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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