Variant report

Variant	rs466108
Chromosome Location	chr5:40796746-40796747
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40793843..40796817-chr5:40803354..40805786,3	K562	blood:
2	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
3	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
4	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
5	chr5:40771614..40774420-chr5:40796699..40798889,2	MCF-7	breast:
6	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
7	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132356	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000212296	Chromatin interaction
ENSG00000113638	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10056345	0.85[ASN][1000 genomes]
rs10060234	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10064175	0.81[ASN][1000 genomes]
rs1070446	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs1097546	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355305	0.85[ASN][1000 genomes]
rs154268	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154275	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154280	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154281	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154284	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171605	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171606	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs192219	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs193864	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs193866	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2008763	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161521	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249413	0.85[ASN][1000 genomes]
rs249414	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs249416	0.87[ASN][1000 genomes]
rs249420	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs249422	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249423	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249425	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249428	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249437	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs249438	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs249441	0.80[ASN][1000 genomes]
rs257009	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569300	0.85[ASN][1000 genomes]
rs29740	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29742	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29743	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29744	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29761	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4277957	0.85[ASN][1000 genomes]
rs4285273	0.85[ASN][1000 genomes]
rs4315964	0.85[ASN][1000 genomes]
rs4315965	0.85[ASN][1000 genomes]
rs432071	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434778	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs4383756	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs447810	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs453037	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457776	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs461404	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466962	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957344	0.85[ASN][1000 genomes]
rs4957351	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59069340	0.85[ASN][1000 genomes]
rs59920139	0.85[ASN][1000 genomes]
rs6451535	0.83[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs6451537	0.85[ASN][1000 genomes]
rs6871999	0.85[ASN][1000 genomes]
rs6896993	0.85[ASN][1000 genomes]
rs6897470	0.83[EUR][1000 genomes]
rs7708680	0.85[ASN][1000 genomes]
rs7711806	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726237	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs7737044	0.85[ASN][1000 genomes]
rs837101	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
4	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs466108	PRKAA1	Cis_1M	lymphoblastoid	RTeQTL
rs466108	FBXO4	cis	parietal	SCAN
rs466108	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs466108	RPL37	cis	cerebellum	SCAN
rs466108		cis	Lymphoblastoid	GTEx
rs466108	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
4	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
8	chr5:40788800-40797400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:40789800-40796800	Weak transcription	Fetal Heart	heart
10	chr5:40790400-40797200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:40790600-40797200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:40792400-40796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:40793600-40796800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr5:40793800-40797000	Weak transcription	Brain Substantia Nigra	brain
15	chr5:40794200-40797200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:40795600-40796800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:40795600-40796800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:40795600-40796800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:40795600-40796800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:40795600-40797000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:40795600-40797200	Enhancers	Primary B cells from peripheral blood	blood
22	chr5:40795600-40797200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr5:40795600-40797200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:40795800-40797400	Weak transcription	Esophagus	oesophagus
25	chr5:40795800-40798600	Active TSS	GM12878-XiMat	blood
26	chr5:40795800-40800000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:40796000-40796800	Enhancers	Fetal Lung	lung
28	chr5:40796000-40797000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr5:40796000-40797200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr5:40796200-40796800	Weak transcription	Psoas Muscle	Psoas
31	chr5:40796200-40796800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:40796200-40797000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:40796200-40797200	Weak transcription	Left Ventricle	heart
34	chr5:40796200-40797200	Weak transcription	Lung	lung
35	chr5:40796200-40797400	Weak transcription	Pancreas	Pancrea
36	chr5:40796200-40799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:40796200-40799600	Active TSS	Fetal Intestine Large	intestine
38	chr5:40796400-40796800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr5:40796400-40796800	Enhancers	Primary T cells from cord blood	blood
40	chr5:40796400-40796800	Flanking Active TSS	Liver	Liver
41	chr5:40796400-40796800	Flanking Active TSS	HepG2	liver
42	chr5:40796400-40796800	Enhancers	HSMM	muscle
43	chr5:40796400-40797000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr5:40796400-40797000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr5:40796400-40797000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:40796400-40797000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:40796400-40797000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:40796400-40797000	Enhancers	Fetal Brain Female	brain
49	chr5:40796400-40797000	Flanking Active TSS	HMEC	breast
50	chr5:40796400-40797200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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