Variant report

Variant	rs2867084
Chromosome Location	chr3:145968552-145968553
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	chr3:145878599..145881384-chr3:145968449..145970595,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10222588	0.81[ASN][1000 genomes]
rs10737947	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10804710	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935611	0.93[ASN][1000 genomes]
rs10935613	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935614	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935615	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935616	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11709096	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11716310	0.92[ASN][1000 genomes]
rs11915448	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11919011	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926517	0.81[ASN][1000 genomes]
rs12487353	0.81[ASN][1000 genomes]
rs12633074	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355570	0.88[EUR][1000 genomes]
rs1398125	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1398529	0.93[ASN][1000 genomes]
rs1512078	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512079	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512080	0.89[ASN][1000 genomes]
rs1512081	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512888	0.92[ASN][1000 genomes]
rs1512890	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512893	0.90[ASN][1000 genomes]
rs1606434	0.89[ASN][1000 genomes]
rs1877511	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1913184	0.92[ASN][1000 genomes]
rs2036980	0.92[ASN][1000 genomes]
rs2175544	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2175545	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867081	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867082	0.89[ASN][1000 genomes]
rs2867083	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903478	0.92[ASN][1000 genomes]
rs2903479	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762686	0.92[ASN][1000 genomes]
rs3762688	0.92[ASN][1000 genomes]
rs3792338	0.92[ASN][1000 genomes]
rs3804648	0.92[ASN][1000 genomes]
rs3804654	0.92[ASN][1000 genomes]
rs3914252	0.92[ASN][1000 genomes]
rs4273339	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4475004	0.90[ASN][1000 genomes]
rs4488802	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4610193	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4681306	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681307	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681308	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681310	0.81[ASN][1000 genomes]
rs6440421	0.93[ASN][1000 genomes]
rs6440422	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770057	0.85[ASN][1000 genomes]
rs6770163	0.93[ASN][1000 genomes]
rs6770278	0.93[ASN][1000 genomes]
rs6775520	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6792732	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800307	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6805377	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7430290	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612683	0.92[ASN][1000 genomes]
rs7621841	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7632412	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633252	0.88[ASN][1000 genomes]
rs7634568	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643778	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645100	0.88[EUR][1000 genomes]
rs907490	0.90[EUR][1000 genomes]
rs9756128	0.92[ASN][1000 genomes]
rs9809892	0.92[ASN][1000 genomes]
rs9813122	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9822280	0.92[ASN][1000 genomes]
rs9825776	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826132	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826360	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826591	0.89[ASN][1000 genomes]
rs9830892	0.89[ASN][1000 genomes]
rs9836419	0.89[ASN][1000 genomes]
rs9838801	0.93[ASN][1000 genomes]
rs9838866	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9839724	0.92[ASN][1000 genomes]
rs9839874	0.92[ASN][1000 genomes]
rs9845890	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850566	0.92[ASN][1000 genomes]
rs9851511	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9855695	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858823	0.90[ASN][1000 genomes]
rs9859273	0.90[ASN][1000 genomes]
rs9863647	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867851	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873891	0.89[ASN][1000 genomes]
rs9875799	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9877004	0.92[ASN][1000 genomes]
rs9881755	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3452197	chr3:145950303-145974111	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3333990	chr3:145950303-145982133	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv998388	chr3:145960954-146087749	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145965400-145969800	Active TSS	Right Atrium	heart
2	chr3:145965600-145969200	Active TSS	Aorta	Aorta
3	chr3:145965800-145969600	Active TSS	NHLF	lung
4	chr3:145966200-145969600	Active TSS	Stomach Smooth Muscle	stomach
5	chr3:145966200-145969800	Active TSS	Colon Smooth Muscle	Colon
6	chr3:145966400-145969400	Active TSS	Fetal Stomach	stomach
7	chr3:145966400-145969800	Active TSS	Ovary	ovary
8	chr3:145966400-145969800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr3:145966600-145969200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:145966600-145969600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:145966800-145969000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:145966800-145969400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:145966800-145969600	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr3:145967200-145969000	Active TSS	Brain Angular Gyrus	brain
15	chr3:145967200-145969400	Active TSS	HUVEC	blood vessel
16	chr3:145967200-145969800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:145967200-145969800	Active TSS	Osteobl	bone
18	chr3:145967800-145968600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:145967800-145968600	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:145967800-145968800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr3:145967800-145969000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:145967800-145969000	Active TSS	Placenta	Placenta
23	chr3:145967800-145969200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr3:145967800-145969200	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr3:145967800-145969200	Active TSS	Brain Anterior Caudate	brain
26	chr3:145967800-145969200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:145967800-145969200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:145967800-145969200	Active TSS	Fetal Kidney	kidney
29	chr3:145967800-145969200	Bivalent/Poised TSS	Thymus	Thymus
30	chr3:145967800-145969400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:145967800-145969400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:145967800-145969400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:145967800-145969400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:145967800-145969400	Active TSS	Psoas Muscle	Psoas
35	chr3:145967800-145969400	Active TSS	HMEC	breast
36	chr3:145967800-145969400	Active TSS	HSMM	muscle
37	chr3:145967800-145969600	Active TSS	Duodenum Mucosa	Duodenum
38	chr3:145967800-145969600	Active TSS	HSMMtube	muscle
39	chr3:145967800-145969800	Active TSS	Brain Substantia Nigra	brain
40	chr3:145967800-145969800	Active TSS	Colonic Mucosa	Colon
41	chr3:145968000-145968600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr3:145968000-145968600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:145968000-145969000	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr3:145968000-145969200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:145968000-145969200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:145968000-145969200	Active TSS	Fetal Lung	lung
47	chr3:145968000-145969200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr3:145968000-145969200	Bivalent/Poised TSS	Stomach Mucosa	stomach
49	chr3:145968000-145969400	Active TSS	Fetal Intestine Large	intestine
50	chr3:145968000-145969400	Active TSS	Fetal Intestine Small	intestine

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