Variant report

Variant	rs9841959
Chromosome Location	chr3:119608157-119608158
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	chr3:119607000..119608720-chr3:119626179..119628022,2	MCF-7	breast:
2	chr3:119606881..119610078-chr3:119812619..119816185,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

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]
rs9837710	0.92[AFR][1000 genomes]
rs9840111	1.00[AFR][1000 genomes]
rs9842216	1.00[AFR][1000 genomes]
rs9842542	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:4 , 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	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
3	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
4	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:119582400-119610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:119582400-119610600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
11	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
12	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
13	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119582600-119609800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:119582600-119610600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:119582600-119611000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:119582600-119611000	Weak transcription	NHLF	lung
18	chr3:119582600-119627200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
20	chr3:119582800-119621200	Weak transcription	Fetal Intestine Large	intestine
21	chr3:119583000-119611000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:119583600-119621400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:119584000-119622800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:119592600-119617800	Weak transcription	Osteobl	bone
26	chr3:119594800-119610800	Weak transcription	Stomach Mucosa	stomach
27	chr3:119597600-119659000	Weak transcription	Gastric	stomach
28	chr3:119598200-119610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:119599800-119611000	Weak transcription	Fetal Kidney	kidney
30	chr3:119599800-119611000	Weak transcription	NH-A	brain
31	chr3:119600000-119610800	Weak transcription	Fetal Brain Male	brain
32	chr3:119600000-119611000	Weak transcription	Adipose Nuclei	Adipose
33	chr3:119601000-119610600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:119601000-119611000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:119603200-119610600	Weak transcription	HSMM	muscle
36	chr3:119603200-119611000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:119603200-119611000	Weak transcription	HMEC	breast
38	chr3:119603400-119611000	Weak transcription	HSMMtube	muscle
39	chr3:119603400-119614600	Weak transcription	NHEK	skin
40	chr3:119603400-119624200	Weak transcription	Hela-S3	cervix
41	chr3:119603600-119624200	Weak transcription	HepG2	liver
42	chr3:119604800-119627800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:119605200-119608600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:119605400-119610200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:119605600-119608600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:119606400-119608400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr3:119606400-119608600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:119606400-119608600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
49	chr3:119606400-119608600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr3:119606400-119608600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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