Variant report

Variant	rs2019562
Chromosome Location	chr12:122250491-122250492
allele	A/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122213805..122214701-chr12:122249630..122250541,6	MCF-7	breast:
2	chr12:122231599..122234135-chr12:122248993..122250611,25	K562	blood:
3	chr12:122249312..122252163-chr12:122325172..122327877,3	K562	blood:
4	chr12:122148543..122152154-chr12:122247522..122251412,4	MCF-7	breast:
5	chr12:122248304..122251064-chr12:132568953..132570962,2	MCF-7	breast:
6	chr12:122213724..122215125-chr12:122249613..122250584,9	K562	blood:
7	chr12:122248762..122251835-chr12:122331420..122334118,3	MCF-7	breast:
8	chr12:122250365..122256158-chr12:122324216..122328328,5	MCF-7	breast:
9	chr12:122247695..122252163-chr12:122325172..122328033,7	K562	blood:
10	chr12:122232209..122233866-chr12:122249576..122251017,11	MCF-7	breast:
11	chr12:122248283..122252969-chr12:122325592..122328736,7	MCF-7	breast:
12	chr12:122220378..122221895-chr12:122249646..122252036,2	K562	blood:
13	chr12:122138274..122140885-chr12:122248656..122250859,2	MCF-7	breast:
14	chr12:122237008..122237974-chr12:122249958..122250519,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000256950	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000185684	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000110801	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1004390	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11043202	0.93[EUR][1000 genomes]
rs11043203	0.93[EUR][1000 genomes]
rs11043207	0.84[EUR][1000 genomes]
rs1168663	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1168664	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168665	0.89[EUR][1000 genomes]
rs1168666	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168668	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1168669	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168671	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168672	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168673	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12307227	0.92[EUR][1000 genomes]
rs12823194	0.81[EUR][1000 genomes]
rs1667578	0.93[EUR][1000 genomes]
rs1667579	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1795965	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1795966	0.81[EUR][1000 genomes]
rs2019561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2122266	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2707066	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2707067	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs712852	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7957564	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974348	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895951	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs895952	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs895953	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs895954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895957	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs921286	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs921287	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs930665	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv911	chr12:122234524-122279425	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2019562	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122243800-122251600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:122247200-122251400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:122247800-122252000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:122248200-122250800	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr12:122248600-122250800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:122248600-122251400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
7	chr12:122248800-122250600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr12:122248800-122250800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
9	chr12:122248800-122251000	Transcr. at gene 5' and 3'	NHEK	skin
10	chr12:122248800-122251200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
11	chr12:122248800-122251200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
12	chr12:122248800-122251200	Transcr. at gene 5' and 3'	NHLF	lung
13	chr12:122248800-122251600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
14	chr12:122249000-122250800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr12:122249000-122250800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:122249000-122250800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
17	chr12:122249000-122250800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr12:122249000-122251000	Transcr. at gene 5' and 3'	Thymus	Thymus
19	chr12:122249000-122251000	Flanking Active TSS	HepG2	liver
20	chr12:122249200-122250600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr12:122249200-122250600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:122249200-122250600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:122249200-122250600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
24	chr12:122249200-122250600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr12:122249200-122250800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr12:122249200-122250800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
27	chr12:122249200-122251000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:122249200-122251000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:122249200-122251200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr12:122249200-122251200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
31	chr12:122249200-122251400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr12:122249200-122251400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:122249200-122251400	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr12:122249400-122250600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:122249400-122250600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
36	chr12:122249400-122250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:122249400-122250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:122249400-122250600	Active TSS	HSMMtube	muscle
39	chr12:122249400-122250800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:122249400-122250800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:122249400-122250800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
42	chr12:122249400-122250800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr12:122249400-122250800	Flanking Active TSS	Liver	Liver
44	chr12:122249400-122250800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
45	chr12:122249400-122250800	Flanking Active TSS	HUVEC	blood vessel
46	chr12:122249400-122251000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:122249400-122251000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr12:122249400-122251000	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr12:122249400-122251200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:122249400-122252000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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