Variant report

Variant	rs58174838
Chromosome Location	chr4:69924309-69924310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10447076	0.80[EUR][1000 genomes]
rs10447077	0.80[EUR][1000 genomes]
rs10452447	0.84[EUR][1000 genomes]
rs12645107	0.89[EUR][1000 genomes]
rs12648462	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17146872	0.86[EUR][1000 genomes]
rs17146900	0.81[EUR][1000 genomes]
rs17147077	0.84[EUR][1000 genomes]
rs17520029	0.82[EUR][1000 genomes]
rs1824266	0.84[EUR][1000 genomes]
rs1841050	0.85[EUR][1000 genomes]
rs1841051	0.85[EUR][1000 genomes]
rs1841054	0.86[EUR][1000 genomes]
rs1973106	0.87[EUR][1000 genomes]
rs2018024	0.85[EUR][1000 genomes]
rs2290764	0.85[EUR][1000 genomes]
rs2290765	0.83[EUR][1000 genomes]
rs2331569	0.81[EUR][1000 genomes]
rs2331570	0.81[EUR][1000 genomes]
rs35470687	0.85[EUR][1000 genomes]
rs4326076	0.93[EUR][1000 genomes]
rs4336293	0.90[EUR][1000 genomes]
rs4467643	0.81[EUR][1000 genomes]
rs4472206	0.93[EUR][1000 genomes]
rs4590113	0.81[EUR][1000 genomes]
rs4604120	0.93[EUR][1000 genomes]
rs4694487	0.83[EUR][1000 genomes]
rs55725814	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57520789	0.83[EUR][1000 genomes]
rs57631654	0.84[EUR][1000 genomes]
rs57955338	0.92[EUR][1000 genomes]
rs58016259	0.85[EUR][1000 genomes]
rs58077880	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58655780	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58878867	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59300882	0.82[EUR][1000 genomes]
rs59449984	0.84[EUR][1000 genomes]
rs59728350	0.85[EUR][1000 genomes]
rs59970425	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61021826	0.85[EUR][1000 genomes]
rs61162302	0.99[EUR][1000 genomes]
rs61174505	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61235442	0.84[EUR][1000 genomes]
rs61416981	0.85[EUR][1000 genomes]
rs6833862	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72851317	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72851318	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72851322	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72851362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72851371	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72851378	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72851379	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72852429	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72852498	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72853561	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72853597	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72855408	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72855411	0.89[EUR][1000 genomes]
rs73826069	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7438042	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7440384	0.81[EUR][1000 genomes]
rs7660744	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7677390	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[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	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69922600-69925000	Enhancers	Fetal Intestine Large	intestine
2	chr4:69922800-69924800	Flanking Active TSS	Liver	Liver
3	chr4:69922800-69925000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr4:69923000-69924600	Flanking Active TSS	HepG2	liver
5	chr4:69923000-69924800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:69923200-69924600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr4:69923200-69924800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr4:69923200-69925000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:69923400-69924400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr4:69923400-69924800	Enhancers	H9 Cell Line	embryonic stem cell
11	chr4:69923600-69924400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:69923600-69924400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:69923600-69924600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:69923600-69924600	Enhancers	Brain Substantia Nigra	brain
15	chr4:69923600-69924800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:69923600-69925000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:69923800-69924400	Enhancers	Brain Anterior Caudate	brain
18	chr4:69923800-69924400	Weak transcription	Colonic Mucosa	Colon
19	chr4:69923800-69924400	Enhancers	Fetal Muscle Leg	muscle
20	chr4:69923800-69924400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr4:69923800-69924600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr4:69923800-69924800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:69923800-69925000	Enhancers	Fetal Kidney	kidney
24	chr4:69923800-69925400	Enhancers	Stomach Mucosa	stomach
25	chr4:69923800-69932400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:69924000-69924400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:69924000-69924400	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr4:69924000-69924400	Enhancers	GM12878-XiMat	blood
29	chr4:69924000-69924600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:69924000-69924600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:69924000-69924600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:69924000-69924800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr4:69924000-69924800	Enhancers	Brain Hippocampus Middle	brain
34	chr4:69924000-69924800	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr4:69924000-69925000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr4:69924000-69925000	Enhancers	Pancreas	Pancrea
37	chr4:69924000-69925200	Enhancers	Fetal Intestine Small	intestine
38	chr4:69924000-69925800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:69924200-69924400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:69924200-69924600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:69924200-69924800	Enhancers	Brain Cingulate Gyrus	brain
42	chr4:69924200-69925000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:69924200-69925000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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