Variant report

Variant	rs1719887
Chromosome Location	chr3:119584627-119584628
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs1154597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13312998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13314595	1.00[CHB][hapmap]
rs1626696	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16830683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs16830689	1.00[CHB][hapmap]
rs1719888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1719889	1.00[CHB][hapmap]
rs1719895	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1732165	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1732169	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs182839	0.82[EUR][1000 genomes]
rs2037547	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461816	0.82[CHB][hapmap]
rs2472680	0.82[CHB][hapmap]
rs3108749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs334534	0.82[EUR][1000 genomes]
rs334551	0.82[EUR][1000 genomes]
rs334552	0.82[EUR][1000 genomes]
rs334554	0.82[EUR][1000 genomes]
rs334561	0.80[EUR][1000 genomes]
rs3853592	0.85[EUR][1000 genomes]
rs4072520	1.00[CHB][hapmap]
rs4438691	0.93[EUR][1000 genomes]
rs4605584	0.89[EUR][1000 genomes]
rs4688043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60272712	0.82[EUR][1000 genomes]
rs6438550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6438555	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6762640	0.85[EUR][1000 genomes]
rs6769435	1.00[CHB][hapmap]
rs6770314	1.00[CHB][hapmap]
rs6771023	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6779828	1.00[CHB][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs6790751	1.00[CHB][hapmap]
rs6797689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs6805931	0.82[EUR][1000 genomes]
rs6807868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7617372	1.00[CHB][hapmap]
rs7620750	0.82[CHB][hapmap]
rs7624540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7628426	0.82[EUR][1000 genomes]
rs7635604	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7650554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7652172	1.00[CHB][hapmap]
rs968824	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9784393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9829763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9851174	1.00[CHB][hapmap]
rs9859778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9879992	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	esv3441832	chr3:119583462-119585585	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119541200-119587000	Weak transcription	Gastric	stomach
2	chr3:119546000-119663400	Weak transcription	Lung	lung
3	chr3:119551400-119594600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:119561200-119591200	Weak transcription	Stomach Mucosa	stomach
5	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
6	chr3:119566800-119586000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:119567000-119605200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
9	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:119575000-119585400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:119575000-119585800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:119575000-119586800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:119575000-119588000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:119577000-119598800	Weak transcription	Fetal Brain Male	brain
15	chr3:119577400-119585200	Strong transcription	Primary B cells from cord blood	blood
16	chr3:119577400-119585200	Strong transcription	HSMM	muscle
17	chr3:119577400-119596600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:119577600-119585400	Weak transcription	K562	blood
19	chr3:119577600-119589400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119577600-119598200	Weak transcription	Left Ventricle	heart
21	chr3:119577600-119602800	Weak transcription	Psoas Muscle	Psoas
22	chr3:119577600-119607600	Weak transcription	Aorta	Aorta
23	chr3:119577800-119607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:119578000-119585600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:119578000-119601400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:119579400-119587000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:119579400-119587000	Strong transcription	Dnd41	blood
28	chr3:119580600-119585000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:119581600-119586600	Strong transcription	HMEC	breast
30	chr3:119581800-119605400	Weak transcription	Colonic Mucosa	Colon
31	chr3:119582400-119586600	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:119582400-119587400	Weak transcription	Brain Substantia Nigra	brain
33	chr3:119582400-119591800	Weak transcription	Placenta	Placenta
34	chr3:119582400-119593600	Weak transcription	Fetal Lung	lung
35	chr3:119582400-119596800	Weak transcription	Fetal Kidney	kidney
36	chr3:119582400-119598400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:119582400-119602200	Weak transcription	A549	lung
38	chr3:119582400-119607400	Weak transcription	Ovary	ovary
39	chr3:119582400-119607600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:119582400-119607600	Weak transcription	Fetal Brain Female	brain
41	chr3:119582400-119607600	Weak transcription	Thymus	Thymus
42	chr3:119582400-119607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:119582400-119610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:119582400-119610600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
46	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
49	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
50	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart

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