Variant report

Variant	rs28489732
Chromosome Location	chr15:59013353-59013354
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	chr15:59007785..59010313-chr15:59010988..59013487,2	K562	blood:
2	chr15:58993902..58996648-chr15:59011876..59013960,2	K562	blood:

Variant related genes	Relation type
ENSG00000199730	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11071391	0.86[AMR][1000 genomes]
rs11071393	0.81[AMR][1000 genomes]
rs12437457	0.84[AMR][1000 genomes]
rs12437952	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12437955	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12437998	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12439231	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440091	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12440267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12441313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441912	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12442451	0.81[AMR][1000 genomes]
rs12442956	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12592332	0.82[AMR][1000 genomes]
rs12900343	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901989	0.84[AMR][1000 genomes]
rs12905110	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906714	0.86[AMR][1000 genomes]
rs12907237	0.86[AMR][1000 genomes]
rs12908261	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908449	0.81[AMR][1000 genomes]
rs12912327	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12917083	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12917500	0.86[AMR][1000 genomes]
rs12917577	0.86[AMR][1000 genomes]
rs1426652	0.84[ASN][1000 genomes]
rs16940587	0.83[AMR][1000 genomes]
rs17236194	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17301954	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2052804	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2052805	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2305421	0.82[AMR][1000 genomes]
rs2414608	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28455654	0.90[AMR][1000 genomes]
rs28470809	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28536555	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28549001	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28576281	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28637832	0.82[AMR][1000 genomes]
rs28722857	0.84[AMR][1000 genomes]
rs28724298	0.82[AMR][1000 genomes]
rs28818840	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35499736	0.87[AMR][1000 genomes]
rs35956992	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6494032	0.80[AMR][1000 genomes]
rs6494034	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494038	0.81[EUR][1000 genomes]
rs7163939	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166076	0.81[AMR][1000 genomes]
rs7167528	0.90[AMR][1000 genomes]
rs7174414	0.81[AMR][1000 genomes]
rs8029805	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8033691	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036448	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9635351	0.82[AMR][1000 genomes]
rs9921024	0.81[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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
3	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:58992000-59015800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:58992000-59023000	Weak transcription	Esophagus	oesophagus
8	chr15:58992000-59023800	Weak transcription	Aorta	Aorta
9	chr15:58992600-59016600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:58992600-59021000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:58994400-59016400	Weak transcription	Adipose Nuclei	Adipose
12	chr15:58996000-59016600	Weak transcription	Colonic Mucosa	Colon
13	chr15:58996200-59016800	Weak transcription	Psoas Muscle	Psoas
14	chr15:58996600-59016600	Weak transcription	NHLF	lung
15	chr15:58996600-59016800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:58998400-59016600	Weak transcription	Osteobl	bone
17	chr15:58998600-59016600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:58998600-59016800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:58999000-59013600	Weak transcription	Right Ventricle	heart
20	chr15:58999000-59023800	Weak transcription	Gastric	stomach
21	chr15:59002400-59016200	Weak transcription	Left Ventricle	heart
22	chr15:59003400-59016400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:59003800-59016600	Weak transcription	NH-A	brain
24	chr15:59004200-59015600	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:59005200-59022400	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:59005600-59021600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:59005600-59023000	Weak transcription	Spleen	Spleen
28	chr15:59005600-59023600	Weak transcription	NHEK	skin
29	chr15:59005800-59022800	Weak transcription	HMEC	breast
30	chr15:59005800-59025200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr15:59006200-59023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:59006200-59024000	Weak transcription	Pancreas	Pancrea
33	chr15:59006400-59014400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:59006400-59016200	Weak transcription	Lung	lung
35	chr15:59006400-59016600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr15:59006400-59016800	Weak transcription	HSMMtube	muscle
37	chr15:59006400-59017000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:59006400-59017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:59006400-59021600	Weak transcription	Fetal Stomach	stomach
40	chr15:59006400-59022800	Weak transcription	Fetal Intestine Small	intestine
41	chr15:59006600-59014800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:59007400-59026400	Weak transcription	Fetal Intestine Large	intestine
43	chr15:59008000-59014600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:59008200-59016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:59008600-59028400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:59009400-59016600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:59009600-59016800	Weak transcription	Stomach Mucosa	stomach
48	chr15:59009600-59029600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:59009800-59016400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr15:59009800-59016600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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