Variant report

Variant	rs6762408
Chromosome Location	chr3:143363222-143363223
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143152690..143153230-chr3:143363138..143363760,2	MCF-7	breast:
2	chr3:143152268..143153220-chr3:143363059..143363930,4	MCF-7	breast:
3	chr3:142648083..142648602-chr3:143363054..143363730,2	MCF-7	breast:
4	chr3:143358392..143360810-chr3:143361757..143363354,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1242065	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1242066	0.80[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1242067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1242068	0.82[ASN][1000 genomes]
rs1242070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1242073	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1242074	0.80[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1242075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1242077	0.83[ASN][1000 genomes]
rs1242079	0.81[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs13101180	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2360865	0.86[JPT][hapmap]
rs56891906	0.85[ASN][1000 genomes]
rs7613679	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143328200-143376200	Weak transcription	Ovary	ovary
2	chr3:143351600-143369800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:143354200-143373600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:143354200-143374000	Weak transcription	Esophagus	oesophagus
5	chr3:143357800-143369000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:143358200-143369000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:143358400-143371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:143360200-143369600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143361400-143373400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:143361600-143364200	Enhancers	Dnd41	blood
11	chr3:143361800-143363600	Enhancers	HUVEC	blood vessel
12	chr3:143361800-143363800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:143362200-143363600	Enhancers	Adipose Nuclei	Adipose
14	chr3:143362200-143363600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:143362200-143363800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:143362400-143363600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:143362400-143364000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:143362600-143363400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:143362600-143363400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr3:143362600-143363400	Enhancers	NHDF-Ad	bronchial
21	chr3:143362600-143363400	Enhancers	NHLF	lung
22	chr3:143362600-143363600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:143362600-143363800	Enhancers	HSMM	muscle
24	chr3:143362600-143364000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:143362800-143363400	Enhancers	Duodenum Mucosa	Duodenum
26	chr3:143362800-143363400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:143362800-143363600	Enhancers	Primary B cells from peripheral blood	blood
28	chr3:143362800-143364000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr3:143362800-143364000	Enhancers	Rectal Smooth Muscle	rectum
30	chr3:143363000-143363400	Enhancers	Stomach Mucosa	stomach
31	chr3:143363000-143363600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:143363000-143363600	Enhancers	Fetal Thymus	thymus
33	chr3:143363000-143364000	Enhancers	Colon Smooth Muscle	Colon
34	chr3:143363000-143364000	Enhancers	Fetal Lung	lung
35	chr3:143363200-143363400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:143363200-143363400	Enhancers	Primary B cells from cord blood	blood
37	chr3:143363200-143363400	Enhancers	Brain Anterior Caudate	brain
38	chr3:143363200-143363400	Enhancers	Brain Cingulate Gyrus	brain
39	chr3:143363200-143363400	Enhancers	Brain Hippocampus Middle	brain
40	chr3:143363200-143363400	Flanking Active TSS	Fetal Kidney	kidney
41	chr3:143363200-143363400	Enhancers	Gastric	stomach
42	chr3:143363200-143363400	Enhancers	NH-A	brain
43	chr3:143363200-143363600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr3:143363200-143363600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:143363200-143363600	Enhancers	Fetal Intestine Small	intestine
46	chr3:143363200-143363600	Enhancers	Fetal Muscle Leg	muscle
47	chr3:143363200-143363600	Enhancers	Fetal Stomach	stomach
48	chr3:143363200-143363600	Enhancers	Psoas Muscle	Psoas
49	chr3:143363200-143363600	Active TSS	Stomach Smooth Muscle	stomach
50	chr3:143363200-143363600	Enhancers	GM12878-XiMat	blood

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