Variant report

Variant	rs4558780
Chromosome Location	chr3:142200764-142200765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10935463	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1129391	0.83[EUR][1000 genomes]
rs11708470	0.91[EUR][1000 genomes]
rs11715514	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11916455	0.91[EUR][1000 genomes]
rs11923612	0.82[EUR][1000 genomes]
rs12629713	0.83[EUR][1000 genomes]
rs12634255	0.83[EUR][1000 genomes]
rs12638158	0.83[EUR][1000 genomes]
rs12639363	0.83[EUR][1000 genomes]
rs13063075	0.86[EUR][1000 genomes]
rs13065800	0.86[EUR][1000 genomes]
rs13066441	0.91[EUR][1000 genomes]
rs13068397	0.83[EUR][1000 genomes]
rs13070239	0.83[EUR][1000 genomes]
rs13072346	0.82[EUR][1000 genomes]
rs13072355	0.83[EUR][1000 genomes]
rs13075259	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13085247	0.91[EUR][1000 genomes]
rs13085261	0.91[EUR][1000 genomes]
rs13089219	0.83[EUR][1000 genomes]
rs13092234	0.81[EUR][1000 genomes]
rs13092593	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13099184	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2227929	0.83[EUR][1000 genomes]
rs2227931	0.91[EUR][1000 genomes]
rs3923464	0.91[EUR][1000 genomes]
rs4256152	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4582075	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440085	0.91[EUR][1000 genomes]
rs6776402	0.83[EUR][1000 genomes]
rs7630115	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636909	0.81[ASN][1000 genomes]
rs7641914	0.81[EUR][1000 genomes]
rs9829125	0.83[ASN][1000 genomes]

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	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
2	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:142170600-142203200	Weak transcription	Spleen	Spleen
4	chr3:142192800-142203000	Weak transcription	Pancreas	Pancrea
5	chr3:142198400-142214400	Weak transcription	Stomach Mucosa	stomach
6	chr3:142198800-142203000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:142199000-142200800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
8	chr3:142199000-142201600	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr3:142199000-142202000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
10	chr3:142199000-142202600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:142199000-142203600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:142199200-142201000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:142199200-142201000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:142199200-142201000	ZNF genes & repeats	Fetal Stomach	stomach
15	chr3:142199200-142201000	Strong transcription	Left Ventricle	heart
16	chr3:142199200-142201200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:142199200-142201200	ZNF genes & repeats	Placenta	Placenta
18	chr3:142199200-142201200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:142199200-142201600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr3:142199200-142201600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:142199200-142201600	ZNF genes & repeats	Esophagus	oesophagus
22	chr3:142199200-142201800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
23	chr3:142199200-142201800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr3:142199200-142201800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr3:142199200-142202000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:142199200-142202000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr3:142199200-142202000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:142199200-142202200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr3:142199200-142202200	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr3:142199200-142202400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:142199200-142202400	ZNF genes & repeats	Dnd41	blood
32	chr3:142199200-142204400	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:142199200-142216000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:142199400-142201000	ZNF genes & repeats	Fetal Thymus	thymus
35	chr3:142199400-142201000	ZNF genes & repeats	Thymus	Thymus
36	chr3:142199400-142201400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
37	chr3:142199400-142201600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
38	chr3:142199400-142201800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:142199400-142202000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:142199400-142202200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr3:142199400-142202200	ZNF genes & repeats	Fetal Intestine Large	intestine
42	chr3:142199600-142200800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:142199600-142200800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:142199600-142201000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr3:142199600-142201400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:142199600-142201400	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr3:142199600-142201600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
48	chr3:142199600-142201600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:142199600-142201600	ZNF genes & repeats	Liver	Liver
50	chr3:142199600-142201600	ZNF genes & repeats	Ovary	ovary

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