Variant report

Variant	rs28818840
Chromosome Location	chr15:59019314-59019315
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59019062..59021030-chr15:59042159..59044868,2	K562	blood:
2	chr15:59017485..59020377-chr15:59047037..59049380,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259173	Chromatin interaction
ENSG00000137845	Chromatin interaction

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

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

rs_ID	r²[population]
rs11071391	0.88[AMR][1000 genomes]
rs11071393	0.83[AMR][1000 genomes]
rs12437457	0.86[AMR][1000 genomes]
rs12437952	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12437955	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12437998	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12439231	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12440091	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12440246	0.81[AMR][1000 genomes]
rs12440267	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441313	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441912	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12442956	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12592332	0.81[AMR][1000 genomes]
rs12592750	0.81[AMR][1000 genomes]
rs12900343	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12901989	0.86[AMR][1000 genomes]
rs12905110	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906714	0.88[AMR][1000 genomes]
rs12907237	0.88[AMR][1000 genomes]
rs12908261	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908449	0.83[AMR][1000 genomes]
rs12912327	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12917083	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12917500	0.88[AMR][1000 genomes]
rs12917577	0.88[AMR][1000 genomes]
rs1426652	0.82[ASN][1000 genomes]
rs16940587	0.81[AMR][1000 genomes]
rs17236194	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17301954	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2052804	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2052805	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2305421	0.84[AMR][1000 genomes]
rs2414608	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28455654	0.92[AMR][1000 genomes]
rs28470809	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28489732	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28536555	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28549001	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28573205	0.81[AMR][1000 genomes]
rs28576281	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28637832	0.81[AMR][1000 genomes]
rs28678478	0.81[AMR][1000 genomes]
rs28722857	0.86[AMR][1000 genomes]
rs28724298	0.81[AMR][1000 genomes]
rs35499736	0.89[AMR][1000 genomes]
rs35956992	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6494034	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494038	0.82[EUR][1000 genomes]
rs7163939	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166076	0.83[AMR][1000 genomes]
rs7167528	0.92[AMR][1000 genomes]
rs7174414	0.83[AMR][1000 genomes]
rs8029805	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033691	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036448	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9635351	0.84[AMR][1000 genomes]
rs9921024	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:58992000-59023000	Weak transcription	Esophagus	oesophagus
4	chr15:58992000-59023800	Weak transcription	Aorta	Aorta
5	chr15:58992600-59021000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:58999000-59023800	Weak transcription	Gastric	stomach
7	chr15:59005200-59022400	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:59005600-59021600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:59005600-59023000	Weak transcription	Spleen	Spleen
10	chr15:59005600-59023600	Weak transcription	NHEK	skin
11	chr15:59005800-59022800	Weak transcription	HMEC	breast
12	chr15:59005800-59025200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:59006200-59023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:59006200-59024000	Weak transcription	Pancreas	Pancrea
15	chr15:59006400-59021600	Weak transcription	Fetal Stomach	stomach
16	chr15:59006400-59022800	Weak transcription	Fetal Intestine Small	intestine
17	chr15:59007400-59026400	Weak transcription	Fetal Intestine Large	intestine
18	chr15:59008600-59028400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:59009600-59029600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:59009800-59021000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:59009800-59035400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:59010000-59021800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:59010200-59024000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:59010200-59024200	Weak transcription	HepG2	liver
25	chr15:59010800-59031200	Weak transcription	Dnd41	blood
26	chr15:59011200-59022400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:59011200-59023800	Weak transcription	Hela-S3	cervix
28	chr15:59013200-59030200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:59013400-59022400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:59013400-59024000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:59013400-59029800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:59015000-59020000	Enhancers	Primary B cells from peripheral blood	blood
33	chr15:59015000-59024200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:59015400-59020200	Enhancers	Primary B cells from cord blood	blood
35	chr15:59016200-59019800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:59016400-59019400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr15:59016600-59020000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr15:59016800-59025000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:59016800-59034200	Weak transcription	Brain Germinal Matrix	brain
40	chr15:59017000-59022400	Weak transcription	Brain Substantia Nigra	brain
41	chr15:59017000-59022800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:59017000-59023800	Weak transcription	Fetal Heart	heart
43	chr15:59017000-59024000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:59017200-59019800	Weak transcription	Brain Angular Gyrus	brain
45	chr15:59017200-59021000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr15:59017200-59021200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:59017200-59021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:59017200-59021200	Weak transcription	Fetal Lung	lung
49	chr15:59017200-59021600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:59017200-59021800	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links