Variant report

Variant	rs58427389
Chromosome Location	chr3:50670793-50670794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50668689..50671062-chr3:50673046..50675259,2	K562	blood:
2	chr3:50668689..50672125-chr3:50673046..50675636,3	K562	blood:
3	chr3:50665308..50667581-chr3:50670455..50672220,2	K562	blood:
4	chr3:50653782..50659891-chr3:50667242..50673193,6	K562	blood:
5	chr3:50653782..50658590-chr3:50669577..50673193,4	K562	blood:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1077215	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12486717	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12487817	0.82[ASN][1000 genomes]
rs12489607	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12491440	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12491812	0.81[ASN][1000 genomes]
rs12492093	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12492540	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12492982	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12494094	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12494326	0.91[ASN][1000 genomes]
rs12494707	0.81[AMR][1000 genomes]
rs12495399	0.82[ASN][1000 genomes]
rs17050991	0.81[ASN][1000 genomes]
rs17050995	0.82[ASN][1000 genomes]
rs17051000	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17051043	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17051045	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17051403	0.87[ASN][1000 genomes]
rs1872184	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1894459	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2035484	0.87[ASN][1000 genomes]
rs2076927	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2170840	0.95[ASN][1000 genomes]
rs2227292	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2227293	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2239750	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2239751	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2239752	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2239753	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2285090	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3749265	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3752449	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3792323	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4476497	0.98[ASN][1000 genomes]
rs4640555	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4688705	0.95[ASN][1000 genomes]
rs4688707	0.91[ASN][1000 genomes]
rs4688709	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4688710	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4688715	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4688716	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs56170012	0.84[ASN][1000 genomes]
rs56856095	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57591074	1.00[EUR][1000 genomes]
rs57910827	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58529408	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59036236	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60552073	0.81[AMR][1000 genomes]
rs60877431	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61193866	0.80[ASN][1000 genomes]
rs61316441	0.91[ASN][1000 genomes]
rs61557316	1.00[EUR][1000 genomes]
rs61574029	0.81[ASN][1000 genomes]
rs61613532	0.82[ASN][1000 genomes]
rs616689	0.98[ASN][1000 genomes]
rs6446208	0.94[ASN][1000 genomes]
rs650655	0.97[ASN][1000 genomes]
rs6771348	0.98[ASN][1000 genomes]
rs6783922	0.98[ASN][1000 genomes]
rs6794155	0.91[ASN][1000 genomes]
rs728902	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72938758	0.82[ASN][1000 genomes]
rs72942785	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72942794	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72944726	0.87[ASN][1000 genomes]
rs72944730	0.87[ASN][1000 genomes]
rs73835531	0.81[ASN][1000 genomes]
rs743753	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs745356	0.98[ASN][1000 genomes]
rs762889	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs808148	0.98[ASN][1000 genomes]
rs876103	0.97[ASN][1000 genomes]
rs876104	0.96[ASN][1000 genomes]
rs876105	0.96[ASN][1000 genomes]
rs9868889	0.98[ASN][1000 genomes]
rs9879397	0.95[ASN][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	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50655400-50677800	Weak transcription	Aorta	Aorta
2	chr3:50655600-50681200	Weak transcription	Fetal Brain Female	brain
3	chr3:50656000-50675600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50656000-50677800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:50660200-50671600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:50660200-50677000	Weak transcription	Liver	Liver
8	chr3:50661400-50671600	Enhancers	Left Ventricle	heart
9	chr3:50661600-50674400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:50661600-50675800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
12	chr3:50662400-50671000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:50662400-50672000	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:50662400-50678200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:50662600-50675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr3:50663200-50677600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:50664200-50672600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr3:50664400-50672800	Genic enhancers	Dnd41	blood
20	chr3:50665200-50674400	Weak transcription	Colonic Mucosa	Colon
21	chr3:50665400-50671000	Genic enhancers	NHEK	skin
22	chr3:50665400-50671200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:50665400-50679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:50665400-50686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:50665600-50673800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:50665600-50675600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:50665600-50686200	Weak transcription	Stomach Mucosa	stomach
28	chr3:50665800-50670800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:50665800-50671200	Enhancers	HMEC	breast
30	chr3:50665800-50672200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:50665800-50674000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:50665800-50675400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:50665800-50675600	Weak transcription	Brain Substantia Nigra	brain
34	chr3:50665800-50675800	Weak transcription	NHLF	lung
35	chr3:50666000-50671800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:50666200-50671400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:50666200-50673600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:50666600-50675400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:50667000-50674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:50667200-50671000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:50667200-50673800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:50667200-50680400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:50667400-50671000	Enhancers	Right Atrium	heart
44	chr3:50667600-50671800	Enhancers	Fetal Heart	heart
45	chr3:50668000-50670800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:50668000-50671400	Enhancers	Placenta	Placenta
47	chr3:50668000-50671800	Enhancers	Primary B cells from cord blood	blood
48	chr3:50668000-50673400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:50668000-50673800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:50668200-50673600	Weak transcription	Duodenum Mucosa	Duodenum

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