Variant report

Variant	rs1535001
Chromosome Location	chr6:34927280-34927281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34918877..34921128-chr6:34926840..34928643,2	K562	blood:
2	chr6:34926256..34928319-chr6:34929581..34931130,2	K562	blood:
3	chr6:34927113..34929243-chr6:34940078..34941859,2	K562	blood:
4	chr6:34927133..34929611-chr6:34935086..34937533,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10947536	0.95[GIH][hapmap]
rs11969436	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13219624	0.81[GIH][hapmap]
rs1737727	0.95[GIH][hapmap]
rs1886243	0.89[ASW][hapmap]
rs1996912	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2140418	0.95[GIH][hapmap]
rs2177381	0.95[GIH][hapmap]
rs2293242	0.95[GIH][hapmap]
rs2473615	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2820232	0.90[JPT][hapmap]
rs2820233	0.90[JPT][hapmap]
rs2820237	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs3817473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823438	0.94[CHD][hapmap];0.90[JPT][hapmap]
rs4646926	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4646949	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6912327	0.86[CEU][hapmap]
rs6923951	0.89[ASW][hapmap]
rs7753949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs847846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847848	0.85[GIH][hapmap]
rs847850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs847851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs847852	0.88[CHD][hapmap]
rs847858	0.85[JPT][hapmap]
rs847859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296139	0.81[GIH][hapmap]
rs9380469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9394248	0.90[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv5257	chr6:34925313-34970101	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv970660	chr6:34925366-34929971	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus and Systemic sclerosis	23740937	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1535001	UHRF1BP1	cis	parietal	SCAN
rs1535001	UHRF1BP1	cis	Adipose Subcutaneous	GTEx
rs1535001	UHRF1BP1	cis	Esophagus Muscularis	GTEx
rs1535001	TAF11	cis	lymphoblastoid	seeQTL
rs1535001	TAF11	cis	cerebellum	SCAN
rs1535001	UHRF1BP1	cis	Muscle Skeletal	GTEx
rs1535001	UHRF1BP1	cis	Artery Tibial	GTEx
rs1535001	C6orf89	cis	parietal	SCAN
rs1535001	TAF11	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34881200-34928200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:34895800-34949200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:34896000-34934600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:34903200-34927800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:34904600-34937400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:34907400-34937600	Weak transcription	Dnd41	blood
7	chr6:34912400-34928000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:34916800-34927800	Weak transcription	Lung	lung
9	chr6:34918600-34938400	Weak transcription	Thymus	Thymus
10	chr6:34919000-34929600	Weak transcription	Fetal Kidney	kidney
11	chr6:34919800-34937200	Weak transcription	NHEK	skin
12	chr6:34920000-34937400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:34920000-34937400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:34920400-34958600	Weak transcription	Colonic Mucosa	Colon
15	chr6:34921200-34937600	Weak transcription	Aorta	Aorta
16	chr6:34921200-34949400	Weak transcription	Esophagus	oesophagus
17	chr6:34921400-34927800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:34921400-34937400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:34921600-34937600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:34921600-34937800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:34921600-34949400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:34921800-34938800	Weak transcription	HMEC	breast
23	chr6:34922000-34928200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:34922000-34953800	Weak transcription	Hela-S3	cervix
25	chr6:34922200-34932200	Weak transcription	Osteobl	bone
26	chr6:34922200-34937400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:34922600-34927600	Weak transcription	Pancreas	Pancrea
28	chr6:34922600-34937400	Weak transcription	HepG2	liver
29	chr6:34922600-34940200	Weak transcription	A549	lung
30	chr6:34922600-34940800	Weak transcription	Stomach Mucosa	stomach
31	chr6:34922800-34937400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:34922800-34950200	Weak transcription	Brain Germinal Matrix	brain
33	chr6:34923600-34928000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:34923600-34928000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:34923600-34936800	Weak transcription	K562	blood
36	chr6:34923800-34929000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:34923800-34937400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:34924200-34928800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:34924200-34929600	Enhancers	Adipose Nuclei	Adipose
40	chr6:34924400-34927600	Enhancers	Brain Hippocampus Middle	brain
41	chr6:34924400-34928200	Enhancers	Fetal Stomach	stomach
42	chr6:34924400-34929000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:34924400-34929600	Enhancers	Right Ventricle	heart
44	chr6:34924600-34927800	Enhancers	Fetal Muscle Leg	muscle
45	chr6:34925000-34927600	Enhancers	Colon Smooth Muscle	Colon
46	chr6:34925000-34937400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:34925200-34937200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:34925600-34927800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:34925600-34927800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:34925600-34932000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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