Variant report

Variant	rs2888298
Chromosome Location	chr3:43335053-43335054
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43326351..43330245-chr3:43331873..43336524,8	MCF-7	breast:
2	chr3:43332997..43335477-chr3:43335619..43338331,2	K562	blood:
3	chr3:43327270..43330892-chr3:43331691..43335794,4	K562	blood:

Variant related genes	Relation type
ENSG00000163788	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10865932	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13065491	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13320571	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075535	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075596	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17075597	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17075600	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2372372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682678	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682679	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682882	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441772	0.81[ASN][1000 genomes]
rs6791641	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6803929	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7649401	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836386	0.91[EUR][1000 genomes];0.84[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	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	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	chr3:43329200-43344800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:43329200-43346800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43329400-43346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:43329600-43345000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:43330400-43344800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:43330800-43336400	Weak transcription	HSMMtube	muscle
7	chr3:43330800-43344600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:43330800-43359000	Weak transcription	Fetal Brain Male	brain
9	chr3:43331000-43335400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:43331000-43340600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:43331000-43344600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:43331200-43338200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:43331200-43344600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:43331400-43338000	Weak transcription	HSMM	muscle
15	chr3:43331400-43338000	Weak transcription	K562	blood
16	chr3:43331400-43344600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:43331400-43344600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:43331400-43358200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:43331600-43335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:43331600-43338200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:43331600-43338200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:43331600-43344600	Weak transcription	Placenta	Placenta
23	chr3:43331600-43344600	Weak transcription	Hela-S3	cervix
24	chr3:43331600-43344800	Weak transcription	Brain Germinal Matrix	brain
25	chr3:43331800-43339600	Enhancers	Liver	Liver
26	chr3:43332000-43336000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr3:43332400-43361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:43332600-43335400	Enhancers	Colon Smooth Muscle	Colon
29	chr3:43332600-43336200	Weak transcription	A549	lung
30	chr3:43332600-43336600	Enhancers	Primary B cells from cord blood	blood
31	chr3:43332800-43336000	Weak transcription	Fetal Kidney	kidney
32	chr3:43332800-43336800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:43332800-43338000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:43332800-43338000	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:43332800-43338200	Weak transcription	Aorta	Aorta
36	chr3:43332800-43339600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:43332800-43339600	Weak transcription	Colonic Mucosa	Colon
38	chr3:43332800-43377000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:43333000-43335200	Enhancers	Adipose Nuclei	Adipose
40	chr3:43333000-43336000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:43333000-43336000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:43333000-43336400	Weak transcription	Fetal Intestine Large	intestine
43	chr3:43333000-43336400	Weak transcription	Fetal Intestine Small	intestine
44	chr3:43333000-43336600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:43333000-43336600	Weak transcription	Small Intestine	intestine
46	chr3:43333000-43336800	Weak transcription	Brain Anterior Caudate	brain
47	chr3:43333000-43338000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr3:43333000-43338000	Enhancers	Primary hematopoietic stem cells	blood
49	chr3:43333000-43338000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:43333000-43338200	Weak transcription	Osteobl	bone

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