Variant report

Variant	rs58835493
Chromosome Location	chr3:48660690-48660691
allele	G/T
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	chr3:48660022-48663466	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48645833..48648564-chr3:48660520..48662280,2	K562	blood:
2	chr3:48660415..48662827-chr3:48667467..48669112,2	K562	blood:
3	chr3:48656876..48658488-chr3:48660227..48663106,2	MCF-7	breast:

Variant related genes	Relation type
TMEM89	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	1.00[EUR][1000 genomes]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[EUR][1000 genomes]
rs28523319	1.00[EUR][1000 genomes]
rs3924179	1.00[EUR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs55782175	1.00[EUR][1000 genomes]
rs58708931	1.00[EUR][1000 genomes]
rs58914641	1.00[EUR][1000 genomes]
rs59352296	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60338814	1.00[EUR][1000 genomes]
rs60352528	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442122	1.00[EUR][1000 genomes]
rs6791777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793732	1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs72930094	1.00[EUR][1000 genomes]
rs72931155	1.00[EUR][1000 genomes]
rs72931157	1.00[EUR][1000 genomes]
rs72931171	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73830478	1.00[EUR][1000 genomes]
rs73831577	1.00[EUR][1000 genomes]
rs73831579	1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	1.00[EUR][1000 genomes]
rs9852211	1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][1000 genomes]
rs9876812	1.00[EUR][1000 genomes]
rs9882714	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48648400-48661200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
3	chr3:48651800-48662400	Weak transcription	NHLF	lung
4	chr3:48655000-48661200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:48655200-48662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:48655400-48662800	Weak transcription	Esophagus	oesophagus
7	chr3:48655400-48662800	Weak transcription	Fetal Brain Female	brain
8	chr3:48655600-48662200	Weak transcription	Fetal Stomach	stomach
9	chr3:48655600-48663000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:48655800-48661200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:48656000-48661200	Weak transcription	Thymus	Thymus
12	chr3:48656000-48662400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:48656000-48664000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:48656200-48662600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:48656400-48663000	Weak transcription	HSMM	muscle
16	chr3:48656400-48663200	Weak transcription	Hela-S3	cervix
17	chr3:48656400-48664400	Weak transcription	HMEC	breast
18	chr3:48656400-48671400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:48656600-48662200	Weak transcription	Osteobl	bone
20	chr3:48656600-48662600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:48656600-48662800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:48656800-48661400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:48656800-48661400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:48656800-48662400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:48656800-48662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:48657200-48661800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:48657200-48664600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:48657400-48662600	Weak transcription	Liver	Liver
29	chr3:48657600-48661000	Weak transcription	Aorta	Aorta
30	chr3:48657600-48661200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:48657600-48661800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:48657600-48662200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:48657600-48662400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:48657800-48661200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:48657800-48661600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:48657800-48661800	Weak transcription	NHEK	skin
37	chr3:48657800-48664200	Weak transcription	Pancreas	Pancrea
38	chr3:48657800-48670000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:48658000-48661400	Weak transcription	Fetal Intestine Large	intestine
40	chr3:48658000-48661600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:48658200-48661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:48658200-48661200	Weak transcription	Colonic Mucosa	Colon
43	chr3:48658200-48661800	Weak transcription	Placenta	Placenta
44	chr3:48658200-48668000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:48658400-48661600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:48658400-48662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:48658400-48662400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:48658600-48661000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:48658600-48661200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:48658600-48661400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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