Variant report

Variant	rs32665
Chromosome Location	chr5:118847140-118847141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10042168	0.82[CHB][hapmap]
rs10045066	0.82[CHB][hapmap]
rs10051019	0.83[CHB][hapmap]
rs10069875	0.83[CHB][hapmap]
rs10073818	0.82[CHB][hapmap]
rs10078097	0.83[CHB][hapmap]
rs10478426	0.83[CHB][hapmap]
rs11241506	0.81[CHB][hapmap]
rs12653056	0.83[CHB][hapmap]
rs12653702	0.83[CHB][hapmap]
rs13361193	0.83[CHB][hapmap]
rs161852	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075698	0.83[CHB][hapmap]
rs2257900	0.96[ASN][1000 genomes]
rs2259347	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2287712	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2303003	0.83[CHB][hapmap]
rs2451816	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs246965	0.85[ASN][1000 genomes]
rs246967	0.85[ASN][1000 genomes]
rs2546210	1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs25640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257970	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.99[ASN][1000 genomes]
rs257971	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257973	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257975	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257978	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs26180	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2636968	0.81[TSI][hapmap]
rs2678070	0.89[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2678091	0.99[ASN][1000 genomes]
rs2945327	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32651	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs32659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35235684	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797363	0.83[CHB][hapmap]
rs3797367	0.82[CHB][hapmap]
rs3850200	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3850202	0.85[ASN][1000 genomes]
rs39971	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs455949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs457106	0.82[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs461108	0.86[CHB][hapmap];0.87[GIH][hapmap]
rs463098	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs463513	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs465091	0.91[CHB][hapmap]
rs4895372	0.91[CHB][hapmap]
rs6875595	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap]
rs6894991	0.83[CHB][hapmap]
rs6895345	0.83[CHB][hapmap]
rs7721602	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]

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	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
2	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
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs32665	HSD17B4	cis	parietal	SCAN
rs32665	PRR16	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118794800-118861200	Weak transcription	HSMM	muscle
2	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:118827600-118847800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:118832400-118878200	Weak transcription	NH-A	brain
6	chr5:118832600-118868600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:118833000-118860200	Weak transcription	Stomach Mucosa	stomach
8	chr5:118834400-118847800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:118836000-118850600	Weak transcription	HUVEC	blood vessel
10	chr5:118838000-118869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:118840200-118878400	Weak transcription	Psoas Muscle	Psoas
12	chr5:118841000-118849800	Weak transcription	Osteobl	bone
13	chr5:118841000-118856600	Strong transcription	Liver	Liver
14	chr5:118841000-118880000	Weak transcription	Brain Germinal Matrix	brain
15	chr5:118841200-118880000	Weak transcription	A549	lung
16	chr5:118841400-118849000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:118841400-118873200	Weak transcription	Fetal Brain Male	brain
18	chr5:118841600-118849000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:118842000-118847800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:118842200-118847400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr5:118842200-118860200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:118842400-118853000	Strong transcription	Adipose Nuclei	Adipose
23	chr5:118842600-118847600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:118842600-118848600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:118843800-118847400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:118843800-118848600	Strong transcription	Fetal Intestine Large	intestine
27	chr5:118843800-118849000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:118843800-118851400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr5:118843800-118852800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:118844000-118847400	Strong transcription	Hela-S3	cervix
31	chr5:118844000-118849600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:118844200-118847600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:118844200-118848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:118844200-118849000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:118844400-118847200	Strong transcription	Primary T cells from cord blood	blood
36	chr5:118844400-118847200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:118844400-118847400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:118844400-118847400	Strong transcription	Left Ventricle	heart
39	chr5:118844400-118847400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:118844400-118847600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr5:118844400-118847600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr5:118844400-118847600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:118844400-118847600	Strong transcription	Dnd41	blood
44	chr5:118844400-118848600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr5:118844400-118852600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:118844400-118852800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:118844600-118847200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:118844600-118847400	Strong transcription	Brain Substantia Nigra	brain
49	chr5:118844800-118847400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:118844800-118847400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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