Variant report

Variant	rs257976
Chromosome Location	chr5:118802385-118802386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2257900	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2257901	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455463	0.82[ASN][1000 genomes]
rs2459726	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs246965	0.80[AMR][1000 genomes]
rs2546210	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257970	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257978	0.92[ASN][1000 genomes]
rs26181	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26184	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2636961	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636962	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636964	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636968	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678070	0.96[ASN][1000 genomes]
rs2678074	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2678076	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2678091	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs27938	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32640	0.90[ASN][1000 genomes]
rs32651	0.96[ASN][1000 genomes]
rs32664	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs382719	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs39970	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs422297	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs426899	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs439954	0.98[ASN][1000 genomes]
rs460274	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463098	0.80[AMR][1000 genomes]
rs463513	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs257976	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118789000-118805000	Weak transcription	Esophagus	oesophagus
2	chr5:118789000-118805400	Weak transcription	Ovary	ovary
3	chr5:118789000-118805400	Weak transcription	Spleen	Spleen
4	chr5:118789000-118811800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:118789000-118813200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:118789000-118826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:118789200-118803800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:118789200-118803800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:118789200-118805000	Weak transcription	Thymus	Thymus
10	chr5:118789200-118805400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:118789200-118805600	Weak transcription	Gastric	stomach
12	chr5:118789200-118813200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:118789400-118803800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:118789400-118805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:118789400-118831200	Weak transcription	NH-A	brain
16	chr5:118789400-118831600	Weak transcription	HSMMtube	muscle
17	chr5:118789600-118802800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:118789600-118804000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:118789600-118810600	Weak transcription	Osteobl	bone
20	chr5:118789600-118812000	Weak transcription	A549	lung
21	chr5:118789600-118813400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:118789600-118813600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:118789800-118803000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:118789800-118804000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:118789800-118805000	Weak transcription	Fetal Stomach	stomach
26	chr5:118789800-118805200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:118789800-118811000	Weak transcription	Brain Angular Gyrus	brain
28	chr5:118789800-118813800	Weak transcription	Fetal Kidney	kidney
29	chr5:118789800-118814400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:118790000-118804000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:118790000-118804200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:118790000-118812600	Weak transcription	Fetal Brain Male	brain
33	chr5:118790200-118813400	Weak transcription	Aorta	Aorta
34	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:118792400-118815000	Weak transcription	K562	blood
36	chr5:118793400-118802400	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:118793400-118802800	Weak transcription	Primary T cells from cord blood	blood
38	chr5:118793400-118802800	Weak transcription	Fetal Lung	lung
39	chr5:118793400-118803800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:118793400-118804200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:118793400-118805000	Weak transcription	Fetal Thymus	thymus
42	chr5:118793400-118810000	Weak transcription	Placenta	Placenta
43	chr5:118793400-118812200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:118794000-118802800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:118794400-118803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:118794800-118861200	Weak transcription	HSMM	muscle
47	chr5:118795000-118803400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:118795200-118802800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:118795200-118813400	Weak transcription	Small Intestine	intestine
50	chr5:118795400-118803400	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links