Variant report

Variant	rs28424211
Chromosome Location	chr3:50017497-50017498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50017458-50017628	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RBM6	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12107362	1.00[AMR][1000 genomes]
rs12107386	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050905	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050921	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17050924	1.00[AMR][1000 genomes]
rs2230592	0.89[AFR][1000 genomes]
rs35340753	0.89[AFR][1000 genomes]
rs55750059	1.00[AMR][1000 genomes]
rs55913179	1.00[AMR][1000 genomes]
rs56057035	0.89[AFR][1000 genomes]
rs56263643	1.00[AMR][1000 genomes]
rs56297242	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56352827	0.87[AFR][1000 genomes]
rs57347154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58095278	1.00[AMR][1000 genomes]
rs58363428	1.00[AMR][1000 genomes]
rs58688714	1.00[AMR][1000 genomes]
rs59822920	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60065407	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60234882	1.00[AMR][1000 genomes]
rs60844685	1.00[AMR][1000 genomes]
rs61156427	1.00[AFR][1000 genomes]
rs61435065	1.00[AMR][1000 genomes]
rs73832783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832789	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832800	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832801	1.00[AMR][1000 genomes]
rs73834118	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834120	1.00[AMR][1000 genomes]
rs73834125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835208	1.00[AMR][1000 genomes]
rs73835216	1.00[AMR][1000 genomes]
rs73835217	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
4	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
6	chr3:49998400-50078600	Weak transcription	K562	blood
7	chr3:49998800-50019600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:49999800-50028400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:50000000-50019600	Strong transcription	Dnd41	blood
10	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:50003000-50033400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:50004400-50027600	Weak transcription	NHEK	skin
13	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:50005000-50027600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:50005000-50031400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:50005000-50036800	Weak transcription	Small Intestine	intestine
17	chr3:50005200-50033400	Weak transcription	Esophagus	oesophagus
18	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
19	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:50005400-50022000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:50005400-50022200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:50005400-50036800	Weak transcription	Brain Anterior Caudate	brain
23	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
24	chr3:50006200-50027800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:50006200-50028200	Weak transcription	Right Ventricle	heart
26	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:50007000-50017600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:50007600-50020000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:50009000-50022800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:50009200-50017800	Strong transcription	Fetal Thymus	thymus
32	chr3:50009200-50018000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:50009200-50018000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:50009400-50017600	Strong transcription	Placenta	Placenta
35	chr3:50010800-50021800	Weak transcription	Gastric	stomach
36	chr3:50010800-50087000	Weak transcription	NHLF	lung
37	chr3:50011000-50022400	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:50011000-50025000	Weak transcription	Ovary	ovary
39	chr3:50011000-50025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:50011000-50031800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:50011000-50036600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:50011000-50036800	Weak transcription	Brain Angular Gyrus	brain
43	chr3:50011000-50037000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:50011000-50041000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:50011000-50046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:50011000-50046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:50011000-50048400	Weak transcription	A549	lung
48	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
49	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon

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