Variant report

Variant	rs9842542
Chromosome Location	chr3:119772793-119772794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119650745..119652304-chr3:119770867..119773862,2	MCF-7	breast:
2	chr3:119772418..119775561-chr3:119813682..119816673,3	K562	blood:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12330290	0.80[AFR][1000 genomes]
rs12330358	0.92[AFR][1000 genomes]
rs12330670	0.92[AFR][1000 genomes]
rs13315412	1.00[AFR][1000 genomes]
rs13316265	0.92[AFR][1000 genomes]
rs13319151	1.00[AFR][1000 genomes]
rs13319559	1.00[AFR][1000 genomes]
rs13319825	1.00[AFR][1000 genomes]
rs13323804	1.00[AFR][1000 genomes]
rs28366921	0.84[AFR][1000 genomes]
rs28481299	0.92[AFR][1000 genomes]
rs28540006	0.92[AFR][1000 genomes]
rs28709836	0.96[AFR][1000 genomes]
rs28817295	1.00[AFR][1000 genomes]
rs6769820	0.92[AFR][1000 genomes]
rs6772172	1.00[AFR][1000 genomes]
rs6778773	1.00[AFR][1000 genomes]
rs6796719	1.00[AFR][1000 genomes]
rs7639665	1.00[AFR][1000 genomes]
rs7639675	1.00[AFR][1000 genomes]
rs9289137	1.00[AFR][1000 genomes]
rs9289139	0.96[AFR][1000 genomes]
rs9810851	1.00[AFR][1000 genomes]
rs9816765	1.00[AFR][1000 genomes]
rs9816864	1.00[AFR][1000 genomes]
rs9819836	0.92[AFR][1000 genomes]
rs9825770	0.92[AFR][1000 genomes]
rs9826355	1.00[AFR][1000 genomes]
rs9835672	1.00[AFR][1000 genomes]
rs9836177	1.00[AFR][1000 genomes]
rs9836325	1.00[AFR][1000 genomes]
rs9840111	1.00[AFR][1000 genomes]
rs9841959	1.00[AFR][1000 genomes]
rs9842216	1.00[AFR][1000 genomes]
rs9843873	0.92[AFR][1000 genomes]
rs9852118	1.00[AFR][1000 genomes]
rs9852797	0.92[AFR][1000 genomes]
rs9854117	1.00[AFR][1000 genomes]
rs9857139	0.88[AFR][1000 genomes]
rs9857548	1.00[AFR][1000 genomes]
rs9858471	1.00[AFR][1000 genomes]
rs9861481	1.00[AFR][1000 genomes]
rs9862099	1.00[AFR][1000 genomes]
rs9864153	1.00[AFR][1000 genomes]
rs9869296	0.84[AFR][1000 genomes]
rs9871701	1.00[AFR][1000 genomes]
rs9871925	1.00[AFR][1000 genomes]
rs9872693	1.00[AFR][1000 genomes]
rs9874110	0.92[AFR][1000 genomes]
rs9880833	0.92[AFR][1000 genomes]
rs9881985	1.00[AFR][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	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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
2	chr3:119760200-119779400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:119760200-119805400	Weak transcription	HMEC	breast
4	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:119768800-119792800	Weak transcription	Fetal Stomach	stomach
6	chr3:119769200-119780600	Weak transcription	Aorta	Aorta
7	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:119769600-119778400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:119769800-119773400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:119769800-119773600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:119769800-119778000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:119769800-119778000	Weak transcription	Adipose Nuclei	Adipose
13	chr3:119769800-119784800	Weak transcription	Dnd41	blood
14	chr3:119770000-119772800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:119770400-119777800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:119770400-119778000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:119770400-119778200	Weak transcription	Stomach Mucosa	stomach
18	chr3:119771200-119778000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:119771400-119778200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:119771400-119778400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:119771400-119779200	Weak transcription	Right Atrium	heart
22	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:119771600-119778000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:119771600-119778200	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:119771600-119778800	Weak transcription	Fetal Heart	heart
26	chr3:119771800-119772800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:119771800-119773000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:119771800-119773200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:119771800-119773200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:119771800-119773800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:119771800-119777800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:119771800-119778000	Weak transcription	Primary T cells from cord blood	blood
33	chr3:119771800-119778200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:119771800-119778400	Weak transcription	NHDF-Ad	bronchial
35	chr3:119771800-119778800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:119771800-119781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:119771800-119783600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:119771800-119805400	Weak transcription	NHEK	skin
39	chr3:119772000-119773600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:119772000-119773800	ZNF genes & repeats	GM12878-XiMat	blood
41	chr3:119772000-119777000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:119772000-119777600	Weak transcription	Psoas Muscle	Psoas
43	chr3:119772000-119778400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:119772000-119779200	Weak transcription	Ovary	ovary
45	chr3:119772200-119772800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:119772200-119773800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:119772200-119774000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:119772200-119775400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:119772200-119776600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:119772200-119778200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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