Variant report

Variant	rs408095
Chromosome Location	chr5:118681650-118681651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118675434..118678874-chr5:118679948..118684456,6	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10059175	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10477585	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1112247	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13155880	0.83[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1396609	0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs17145265	0.92[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs250298	0.92[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs250299	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs250308	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32653	0.86[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs32655	0.93[AFR][1000 genomes]
rs32657	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs32658	0.88[ASW][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3797339	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3797341	0.80[AFR][1000 genomes]
rs3797343	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs3813308	0.88[ASW][hapmap];0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3920174	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461108	0.82[GIH][hapmap]
rs4895372	0.81[JPT][hapmap]
rs6863311	0.82[AFR][1000 genomes]
rs6864305	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6869512	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6870253	0.87[YRI][hapmap]
rs6875595	0.82[GIH][hapmap]
rs6876224	0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6877025	0.89[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6882237	0.82[AFR][1000 genomes]
rs6896277	0.81[AFR][1000 genomes]
rs6896553	0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6896559	0.81[AFR][1000 genomes]
rs7707470	0.84[AFR][1000 genomes]
rs7721602	0.80[GIH][hapmap]
rs996934	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[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	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs408095	HSD17B4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118695400	Weak transcription	A549	lung
3	chr5:118673200-118683600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:118673200-118683800	Weak transcription	Hela-S3	cervix
5	chr5:118673400-118683000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:118673800-118683400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:118674200-118681800	Weak transcription	Pancreas	Pancrea
8	chr5:118674200-118689000	Weak transcription	Esophagus	oesophagus
9	chr5:118674400-118689000	Weak transcription	Gastric	stomach
10	chr5:118676000-118682400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:118676200-118681800	Weak transcription	Spleen	Spleen
12	chr5:118676600-118681800	Weak transcription	Right Atrium	heart
13	chr5:118676800-118681800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:118676800-118689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:118676800-118691400	Weak transcription	Lung	lung
16	chr5:118677000-118686000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:118677200-118686800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:118677400-118682600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr5:118677800-118681800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr5:118677800-118681800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:118677800-118683400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:118678000-118681800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:118678000-118690600	Weak transcription	NHEK	skin
24	chr5:118678200-118682200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:118678200-118682600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:118678200-118682600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:118678200-118683400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:118678200-118684600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:118678400-118682000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:118678600-118681800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:118678600-118681800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:118678800-118683600	Weak transcription	Adipose Nuclei	Adipose
33	chr5:118678800-118686400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:118679000-118682600	Genic enhancers	Primary B cells from cord blood	blood
35	chr5:118679000-118683400	Weak transcription	K562	blood
36	chr5:118679000-118683400	Weak transcription	NHLF	lung
37	chr5:118679000-118690600	Weak transcription	Fetal Intestine Small	intestine
38	chr5:118679000-118690800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:118679200-118681800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:118679600-118683200	Weak transcription	Fetal Heart	heart
41	chr5:118679600-118683600	Weak transcription	Fetal Kidney	kidney
42	chr5:118679800-118683400	Weak transcription	NHDF-Ad	bronchial
43	chr5:118679800-118683800	Weak transcription	Fetal Lung	lung
44	chr5:118679800-118689400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:118680000-118683600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:118680200-118681800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:118680200-118681800	Weak transcription	Left Ventricle	heart
48	chr5:118680200-118681800	Weak transcription	Dnd41	blood
49	chr5:118680200-118682800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr5:118680200-118683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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