Variant report

Variant	rs58000475
Chromosome Location	chr15:52302161-52302162
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52300735..52303050-chr15:52304162..52305762,3	MCF-7	breast:
2	chr15:52261811..52265518-chr15:52298759..52302877,5	MCF-7	breast:
3	chr15:52301522..52303916-chr15:52390300..52393183,2	MCF-7	breast:
4	chr15:52273041..52275862-chr15:52300749..52303075,2	MCF-7	breast:
5	chr15:52295795..52300731-chr15:52301222..52304726,5	MCF-7	breast:
6	chr15:52263196..52265613-chr15:52299179..52302350,3	MCF-7	breast:
7	chr15:52293032..52297316-chr15:52297348..52303144,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000259712	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152141	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10518675	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16964694	0.90[ASN][1000 genomes]
rs16964700	0.90[ASN][1000 genomes]
rs16964705	0.90[ASN][1000 genomes]
rs16964720	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17612255	0.86[ASN][1000 genomes]
rs2001741	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017967	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2246726	0.88[ASN][1000 genomes]
rs2306793	0.86[EUR][1000 genomes]
rs2414120	0.86[ASN][1000 genomes]
rs2414123	0.90[ASN][1000 genomes]
rs2441779	0.88[ASN][1000 genomes]
rs2470593	0.88[ASN][1000 genomes]
rs2470594	0.88[ASN][1000 genomes]
rs2470595	0.91[ASN][1000 genomes]
rs2554340	0.86[ASN][1000 genomes]
rs2899484	0.86[EUR][1000 genomes]
rs3099571	0.86[ASN][1000 genomes]
rs4375608	0.93[ASN][1000 genomes]
rs4456445	0.93[ASN][1000 genomes]
rs4774606	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775993	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4775995	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775996	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55705935	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55714716	0.95[ASN][1000 genomes]
rs55873482	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56307802	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56677715	0.98[ASN][1000 genomes]
rs58936667	0.81[ASN][1000 genomes]
rs61546369	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7177328	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7359204	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74013636	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013638	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74013640	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74013641	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74013642	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74013644	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013645	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013646	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013647	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013648	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013653	0.90[ASN][1000 genomes]
rs74013654	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74013656	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74013657	0.86[ASN][1000 genomes]
rs74013661	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7497554	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs751560	0.90[ASN][1000 genomes]
rs8033365	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033840	0.88[ASN][1000 genomes]
rs8036048	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8041281	0.88[ASN][1000 genomes]
rs9796534	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	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52293000-52303200	Weak transcription	Pancreas	Pancrea
2	chr15:52293400-52303200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:52296600-52303400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:52297800-52304400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:52298400-52302400	Enhancers	K562	blood
6	chr15:52299000-52304200	Weak transcription	Psoas Muscle	Psoas
7	chr15:52299200-52304200	Weak transcription	Fetal Heart	heart
8	chr15:52299400-52303000	Weak transcription	HSMM	muscle
9	chr15:52299400-52303200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:52299400-52303200	Weak transcription	NHDF-Ad	bronchial
11	chr15:52299400-52303200	Weak transcription	NHLF	lung
12	chr15:52299400-52310800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:52299600-52302200	Weak transcription	NHEK	skin
14	chr15:52299600-52302800	Weak transcription	HMEC	breast
15	chr15:52299600-52303000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:52299600-52303000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:52299600-52303000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:52299600-52303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:52299600-52303000	Weak transcription	NH-A	brain
20	chr15:52299600-52303000	Weak transcription	Osteobl	bone
21	chr15:52299600-52303200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:52299600-52303200	Weak transcription	Right Atrium	heart
23	chr15:52299600-52303400	Weak transcription	Esophagus	oesophagus
24	chr15:52299600-52303400	Weak transcription	Left Ventricle	heart
25	chr15:52299600-52304000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:52299600-52305400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:52299600-52305600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:52299600-52310200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:52299600-52310600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:52299600-52310800	Weak transcription	HSMMtube	muscle
31	chr15:52299800-52303200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:52300800-52303000	Enhancers	Hela-S3	cervix
33	chr15:52301000-52302800	Weak transcription	Lung	lung
34	chr15:52301200-52302400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:52301200-52303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:52301200-52305400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:52301200-52305600	Weak transcription	Primary T cells from cord blood	blood
38	chr15:52301400-52310800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:52301400-52310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:52301400-52310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:52301400-52310800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:52301600-52303000	Weak transcription	Stomach Mucosa	stomach
43	chr15:52301600-52303200	Weak transcription	Brain Angular Gyrus	brain
44	chr15:52301600-52303200	Weak transcription	Brain Anterior Caudate	brain
45	chr15:52301600-52303200	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:52301600-52303400	Weak transcription	Adipose Nuclei	Adipose
47	chr15:52301600-52303400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:52301600-52303400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:52301600-52304000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:52301600-52304000	Weak transcription	Small Intestine	intestine

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