Variant report

Variant	rs6779828
Chromosome Location	chr3:119775147-119775148
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	chr3:119774518..119780956-chr3:119811182..119816004,10	MCF-7	breast:
2	chr3:119772418..119775561-chr3:119813682..119816673,3	K562	blood:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1154596	1.00[CHB][hapmap]
rs1154597	1.00[CHB][hapmap]
rs11921053	0.91[EUR][1000 genomes]
rs13312998	1.00[CHB][hapmap]
rs13314595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1579031	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16830683	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs16830689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719887	1.00[CHB][hapmap]
rs1719888	1.00[CHB][hapmap]
rs1719889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1719895	1.00[CHB][hapmap]
rs1732170	0.82[CEU][hapmap]
rs182839	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs184576	0.82[ASN][1000 genomes]
rs28516957	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108749	1.00[CHB][hapmap]
rs334533	0.82[CEU][hapmap]
rs334534	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs334535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334552	0.84[ASN][1000 genomes]
rs334554	0.84[ASN][1000 genomes]
rs334559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334560	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs334561	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs334566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4072520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4450859	0.82[AMR][1000 genomes]
rs4688043	1.00[CHB][hapmap]
rs56126162	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58043853	0.91[EUR][1000 genomes]
rs6438554	1.00[CHB][hapmap]
rs6438555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66650215	0.82[EUR][1000 genomes]
rs6769435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6771023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs6774693	0.98[EUR][1000 genomes]
rs6775397	0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6784239	1.00[CHB][hapmap]
rs6785050	1.00[CHB][hapmap]
rs6790751	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6795874	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6797689	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6802301	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805931	0.84[ASN][1000 genomes]
rs6807868	1.00[CHB][hapmap]
rs7613197	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7620750	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7624540	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7628426	0.84[ASN][1000 genomes]
rs7636600	0.93[EUR][1000 genomes]
rs7644234	0.82[CEU][hapmap]
rs7649661	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7650554	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7652172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289138	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs968824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9829763	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9851174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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:55 , 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	chr3:119769800-119778000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:119769800-119778000	Weak transcription	Adipose Nuclei	Adipose
11	chr3:119769800-119784800	Weak transcription	Dnd41	blood
12	chr3:119770400-119777800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:119770400-119778000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:119770400-119778200	Weak transcription	Stomach Mucosa	stomach
15	chr3:119771200-119778000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:119771400-119778200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:119771400-119778400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:119771400-119779200	Weak transcription	Right Atrium	heart
19	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:119771600-119778000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:119771600-119778200	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:119771600-119778800	Weak transcription	Fetal Heart	heart
23	chr3:119771800-119777800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:119771800-119778000	Weak transcription	Primary T cells from cord blood	blood
25	chr3:119771800-119778200	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:119771800-119778400	Weak transcription	NHDF-Ad	bronchial
27	chr3:119771800-119778800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:119771800-119781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:119771800-119783600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:119771800-119805400	Weak transcription	NHEK	skin
31	chr3:119772000-119777000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:119772000-119777600	Weak transcription	Psoas Muscle	Psoas
33	chr3:119772000-119778400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:119772000-119779200	Weak transcription	Ovary	ovary
35	chr3:119772200-119775400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:119772200-119776600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:119772200-119778200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:119772400-119776600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:119772400-119777800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:119772400-119778800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:119772800-119775200	Weak transcription	Left Ventricle	heart
42	chr3:119772800-119777800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
44	chr3:119773600-119775200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:119773800-119775800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:119773800-119776400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:119773800-119777200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:119773800-119777800	Weak transcription	Brain Angular Gyrus	brain
49	chr3:119773800-119787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:119774000-119776400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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