Variant report

Variant	rs58648683
Chromosome Location	chr12:122125178-122125179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122125125..122127616-chr12:122187006..122188687,2	K562	blood:
2	chr12:122064331..122066305-chr12:122123658..122126561,2	MCF-7	breast:
3	chr12:121788975..121791215-chr12:122123232..122125237,2	K562	blood:
4	chr12:122115091..122119007-chr12:122123231..122126528,5	K562	blood:
5	chr12:122124453..122127425-chr12:122127713..122130672,3	K562	blood:
6	chr12:122114958..122116591-chr12:122123026..122125296,2	K562	blood:
7	chr12:122122153..122127459-chr12:122235506..122240049,10	MCF-7	breast:
8	chr12:121931227..121933297-chr12:122123567..122126169,2	K562	blood:
9	chr12:122123146..122128451-chr12:122240721..122245772,6	MCF-7	breast:
10	chr12:122125178..122127616-chr12:122187006..122188526,2	K562	blood:
11	chr12:122123518..122126727-chr12:122231097..122233939,3	MCF-7	breast:
12	chr12:122017543..122019584-chr12:122124847..122126466,2	K562	blood:
13	chr12:122101998..122103824-chr12:122123372..122125942,2	K562	blood:
14	chr12:122063044..122066006-chr12:122123378..122126114,2	MCF-7	breast:
15	chr12:122125009..122127418-chr12:122238463..122240400,2	K562	blood:
16	chr12:122103388..122106454-chr12:122121633..122126620,5	K562	blood:
17	chr12:122125045..122125638-chr12:122231767..122232417,2	K562	blood:
18	chr12:122123533..122126462-chr12:122235379..122238113,4	K562	blood:
19	chr12:122125017..122126600-chr12:122240555..122242407,2	MCF-7	breast:
20	chr12:122124832..122127542-chr12:122129875..122131876,2	MCF-7	breast:
21	chr12:122062918..122065816-chr12:122124530..122126213,2	K562	blood:
22	chr12:122125119..122128228-chr12:122229957..122233821,5	MCF-7	breast:
23	chr12:122123715..122126577-chr12:122127730..122130596,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM120B-2	chr12:122125156-122125192	NONHSAT031436

No data

Variant related genes	Relation type
ENSG00000272849	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000256742	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11833075	0.95[ASN][1000 genomes]
rs35343615	1.00[EUR][1000 genomes]
rs4760119	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760120	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760122	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760124	1.00[EUR][1000 genomes]
rs55692746	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55699326	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55911302	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56166919	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56790499	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57099146	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57195740	1.00[EUR][1000 genomes]
rs59143714	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59976026	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60637634	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227927	1.00[EUR][1000 genomes]
rs73227935	1.00[EUR][1000 genomes]
rs73227941	1.00[EUR][1000 genomes]
rs73227943	1.00[EUR][1000 genomes]
rs73227944	1.00[EUR][1000 genomes]
rs73227945	1.00[EUR][1000 genomes]
rs73227946	0.93[EUR][1000 genomes]
rs73227949	1.00[EUR][1000 genomes]
rs73227954	1.00[EUR][1000 genomes]
rs7397580	0.83[EUR][1000 genomes]
rs7486943	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer 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	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122117000-122125800	Weak transcription	K562	blood
2	chr12:122121800-122149600	Weak transcription	Right Atrium	heart
3	chr12:122123800-122125200	Enhancers	Primary T cells from cord blood	blood
4	chr12:122123800-122125600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:122124200-122125400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr12:122124200-122125400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:122124200-122125400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:122124400-122125400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr12:122124400-122125400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:122124400-122125400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:122124400-122125400	Active TSS	Muscle Satellite Cultured Cells	--
12	chr12:122124400-122125400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr12:122124400-122125400	Enhancers	Fetal Lung	lung
14	chr12:122124400-122125400	Enhancers	GM12878-XiMat	blood
15	chr12:122124400-122125400	Active TSS	HSMMtube	muscle
16	chr12:122124400-122125400	Active TSS	NHDF-Ad	bronchial
17	chr12:122124400-122125400	Active TSS	Osteobl	bone
18	chr12:122124600-122125200	Active TSS	Fetal Muscle Leg	muscle
19	chr12:122124600-122125400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:122124600-122125400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:122124600-122125400	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:122124600-122125400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:122124600-122125400	Active TSS	Brain Anterior Caudate	brain
24	chr12:122124600-122125400	Active TSS	Brain Cingulate Gyrus	brain
25	chr12:122124600-122125400	Active TSS	Brain Hippocampus Middle	brain
26	chr12:122124600-122125400	Active TSS	Fetal Brain Female	brain
27	chr12:122124600-122125400	Active TSS	Stomach Smooth Muscle	stomach
28	chr12:122124600-122125400	Active TSS	Thymus	Thymus
29	chr12:122124600-122125600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:122124600-122129000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:122124800-122125200	Active TSS	Primary B cells from cord blood	blood
32	chr12:122124800-122125200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:122124800-122125200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:122124800-122125200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:122124800-122125400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:122124800-122125400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:122124800-122125400	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr12:122124800-122125400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:122124800-122125400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:122124800-122125400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:122124800-122125400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:122124800-122125400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:122124800-122125400	Active TSS	Brain Angular Gyrus	brain
44	chr12:122124800-122125400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:122124800-122125400	Active TSS	Brain Substantia Nigra	brain
46	chr12:122124800-122125400	Active TSS	Fetal Kidney	kidney
47	chr12:122124800-122125600	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr12:122125000-122125200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:122125000-122125200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr12:122125000-122125200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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