Variant report

Variant	rs62263597
Chromosome Location	chr3:50131691-50131692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50131320..50133089-chr3:50157321..50159844,2	K562	blood:
2	chr3:50126047..50129250-chr3:50131237..50134548,5	K562	blood:
3	chr3:50125097..50128236-chr3:50128554..50131975,3	MCF-7	breast:
4	chr3:50130138..50132585-chr3:50151323..50154093,2	K562	blood:
5	chr3:50126047..50131036-chr3:50131245..50135023,6	K562	blood:
6	chr3:50131279..50132784-chr3:50275487..50276987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000003756	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11130237	0.89[AMR][1000 genomes]
rs11130240	0.83[AMR][1000 genomes]
rs11916999	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11920034	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11924670	0.88[ASN][1000 genomes]
rs11924711	0.88[ASN][1000 genomes]
rs11928995	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486470	0.88[ASN][1000 genomes]
rs12486808	0.83[AMR][1000 genomes]
rs12490944	0.83[AMR][1000 genomes]
rs12492291	0.88[ASN][1000 genomes]
rs12494077	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12494172	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12494916	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12495114	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12629129	0.83[AMR][1000 genomes]
rs12629677	0.83[AMR][1000 genomes]
rs12631248	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12631306	0.83[AMR][1000 genomes]
rs12631309	0.83[AMR][1000 genomes]
rs12632751	0.88[ASN][1000 genomes]
rs12636045	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636232	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636669	0.83[AMR][1000 genomes]
rs12637222	0.83[AMR][1000 genomes]
rs12637457	0.83[AMR][1000 genomes]
rs12638046	0.83[AMR][1000 genomes]
rs13100903	0.82[ASN][1000 genomes]
rs1317215	0.82[AMR][1000 genomes]
rs13326300	0.82[AMR][1000 genomes]
rs2023951	0.88[ASN][1000 genomes]
rs2023952	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28478136	0.82[AMR][1000 genomes]
rs35333166	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57009357	0.83[AMR][1000 genomes]
rs59802870	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61491513	0.83[AMR][1000 genomes]
rs61729114	0.83[AMR][1000 genomes]
rs62260756	0.82[AMR][1000 genomes]
rs62260770	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260771	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62262060	0.82[AMR][1000 genomes]
rs62262096	0.83[AMR][1000 genomes]
rs62262099	0.83[AMR][1000 genomes]
rs62262104	0.83[AMR][1000 genomes]
rs62262116	0.83[AMR][1000 genomes]
rs62262138	0.83[AMR][1000 genomes]
rs62262144	0.83[AMR][1000 genomes]
rs62263578	0.83[AMR][1000 genomes]
rs62263584	0.88[ASN][1000 genomes]
rs62263586	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62263588	0.88[ASN][1000 genomes]
rs62263590	0.88[ASN][1000 genomes]
rs62263591	0.88[ASN][1000 genomes]
rs62263596	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62263600	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797500	0.82[AMR][1000 genomes]
rs9859813	0.82[AMR][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	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
2	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking 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	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50127400-50132800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:50127400-50150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:50127800-50157800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr3:50128000-50134600	Strong transcription	Esophagus	oesophagus
5	chr3:50128000-50152600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:50128000-50157800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:50128000-50158000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:50128000-50158000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr3:50128200-50134600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:50128200-50135000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:50128200-50152800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:50128200-50158800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:50128400-50132000	Strong transcription	Left Ventricle	heart
14	chr3:50128400-50148800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:50128400-50157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:50128400-50158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:50128400-50158400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:50128400-50159000	Strong transcription	Lung	lung
19	chr3:50128600-50131800	Strong transcription	NHDF-Ad	bronchial
20	chr3:50128600-50132000	Strong transcription	Right Ventricle	heart
21	chr3:50128600-50132400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:50128600-50134600	Strong transcription	Aorta	Aorta
23	chr3:50128600-50137400	Weak transcription	Right Atrium	heart
24	chr3:50128600-50137400	Strong transcription	HSMM	muscle
25	chr3:50128600-50137400	Strong transcription	HSMMtube	muscle
26	chr3:50128600-50138000	Strong transcription	Small Intestine	intestine
27	chr3:50128600-50141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:50128600-50148800	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:50128600-50156200	Strong transcription	Ovary	ovary
30	chr3:50128600-50158000	Strong transcription	NH-A	brain
31	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
35	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
37	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
39	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
40	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:50128600-50159200	Strong transcription	Liver	Liver
43	chr3:50128600-50159200	Strong transcription	NHEK	skin
44	chr3:50128600-50160400	Strong transcription	Fetal Thymus	thymus
45	chr3:50128800-50134600	Strong transcription	Fetal Kidney	kidney
46	chr3:50128800-50137400	Strong transcription	Fetal Lung	lung
47	chr3:50128800-50149000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:50128800-50156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:50128800-50156600	Strong transcription	Brain Substantia Nigra	brain
50	chr3:50128800-50158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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