Variant report

Variant	rs28493566
Chromosome Location	chr4:88373131-88373132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88023177..88025115-chr4:88372900..88374503,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10000196	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10009948	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10023606	0.95[ASN][1000 genomes]
rs10024781	0.96[ASN][1000 genomes]
rs10030035	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10032122	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10084883	0.99[ASN][1000 genomes]
rs12640451	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640894	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648665	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12650763	0.99[ASN][1000 genomes]
rs12651034	0.99[ASN][1000 genomes]
rs28366407	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28415220	0.91[ASN][1000 genomes]
rs28437709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493315	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28529046	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28535549	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696943	0.88[ASN][1000 genomes]
rs28712618	0.99[ASN][1000 genomes]
rs28718986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28762371	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28805573	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34027531	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4411944	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55824708	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56153912	0.97[ASN][1000 genomes]
rs58192677	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67121411	0.94[ASN][1000 genomes]
rs68045074	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72652067	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665115	0.95[ASN][1000 genomes]
rs7673763	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7677249	0.95[ASN][1000 genomes]
rs7680878	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7690728	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9995987	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9998212	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	nsv1011882	chr4:88363959-88402477	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28493566	HSD17B11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88344400-88398600	Weak transcription	Gastric	stomach
2	chr4:88345200-88400000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:88345200-88416400	Weak transcription	Colonic Mucosa	Colon
4	chr4:88345400-88378800	Weak transcription	A549	lung
5	chr4:88346200-88382600	Weak transcription	NHLF	lung
6	chr4:88346400-88379400	Weak transcription	Small Intestine	intestine
7	chr4:88346600-88410400	Weak transcription	Esophagus	oesophagus
8	chr4:88349000-88375400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:88349400-88381800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:88350600-88380600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:88351200-88379000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:88351400-88382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:88351600-88414600	Weak transcription	Psoas Muscle	Psoas
14	chr4:88352600-88387200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:88353400-88377000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:88354800-88381600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:88356000-88377600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:88356400-88376400	Strong transcription	Liver	Liver
19	chr4:88356400-88377200	Weak transcription	Fetal Brain Male	brain
20	chr4:88356600-88382000	Weak transcription	Brain Germinal Matrix	brain
21	chr4:88357600-88380000	Weak transcription	Brain Angular Gyrus	brain
22	chr4:88357800-88381600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:88359800-88382200	Weak transcription	Fetal Brain Female	brain
24	chr4:88360400-88381800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:88360800-88373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:88361200-88383000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:88363400-88375600	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:88363400-88380600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:88363600-88374400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:88364400-88373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:88364400-88375400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:88364400-88377400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:88364400-88379000	Weak transcription	Brain Substantia Nigra	brain
34	chr4:88364800-88377400	Weak transcription	HepG2	liver
35	chr4:88364800-88382800	Weak transcription	HMEC	breast
36	chr4:88365000-88380800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:88365000-88403400	Weak transcription	Right Ventricle	heart
38	chr4:88365200-88381800	Weak transcription	HUVEC	blood vessel
39	chr4:88366000-88381400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:88366600-88379000	Weak transcription	Fetal Kidney	kidney
41	chr4:88366600-88382400	Weak transcription	Fetal Heart	heart
42	chr4:88367400-88380800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:88367400-88381600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr4:88367800-88377400	Weak transcription	Pancreas	Pancrea
45	chr4:88368800-88375400	Strong transcription	Fetal Intestine Small	intestine
46	chr4:88369400-88376400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:88369600-88373800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:88370200-88376600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:88370200-88380200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:88370400-88373800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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