Variant report

Variant	rs28437709
Chromosome Location	chr4:88371941-88371942
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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]
rs28493315	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28493566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs28437709	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	chr4:88345400-88372400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:88345400-88378800	Weak transcription	A549	lung
6	chr4:88345800-88372200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:88346200-88382600	Weak transcription	NHLF	lung
8	chr4:88346400-88372200	Weak transcription	Aorta	Aorta
9	chr4:88346400-88379400	Weak transcription	Small Intestine	intestine
10	chr4:88346600-88372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:88346600-88410400	Weak transcription	Esophagus	oesophagus
12	chr4:88347200-88372000	Weak transcription	NHEK	skin
13	chr4:88349000-88372400	Weak transcription	HSMMtube	muscle
14	chr4:88349000-88375400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:88349400-88381800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:88350600-88380600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:88351200-88379000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:88351400-88382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:88351600-88414600	Weak transcription	Psoas Muscle	Psoas
20	chr4:88352600-88387200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:88353400-88377000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:88354800-88381600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:88356000-88377600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:88356400-88376400	Strong transcription	Liver	Liver
25	chr4:88356400-88377200	Weak transcription	Fetal Brain Male	brain
26	chr4:88356600-88382000	Weak transcription	Brain Germinal Matrix	brain
27	chr4:88357600-88372000	Weak transcription	Hela-S3	cervix
28	chr4:88357600-88380000	Weak transcription	Brain Angular Gyrus	brain
29	chr4:88357800-88381600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr4:88359800-88382200	Weak transcription	Fetal Brain Female	brain
31	chr4:88360400-88381800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:88360600-88372000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:88360800-88373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:88361200-88383000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:88361800-88372200	Weak transcription	Ovary	ovary
36	chr4:88363400-88375600	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:88363400-88380600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:88363600-88372200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:88363600-88374400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:88363800-88372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:88364400-88372200	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:88364400-88373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:88364400-88375400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:88364400-88377400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:88364400-88379000	Weak transcription	Brain Substantia Nigra	brain
46	chr4:88364800-88372000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:88364800-88372200	Weak transcription	Brain Anterior Caudate	brain
48	chr4:88364800-88377400	Weak transcription	HepG2	liver
49	chr4:88364800-88382800	Weak transcription	HMEC	breast
50	chr4:88365000-88372000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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