Variant report

Variant	rs6694817
Chromosome Location	chr1:154401972-154401973
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	chr1:154401123..154404227-chr1:154404483..154407452,3	MCF-7	breast:
2	chr1:154378359..154380579-chr1:154401148..154402901,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10908837	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908838	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265611	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11265612	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117832	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118721	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12118770	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12129500	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4537545	0.88[ASW][hapmap]
rs4553185	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4601580	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4845371	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845619	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845623	0.94[ASW][hapmap]
rs4845625	0.94[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59632925	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427658	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667434	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6683206	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6686750	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6687726	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689306	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689393	0.94[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6694258	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7526131	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7529229	0.88[ASW][hapmap]
rs7536152	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7549250	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549338	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553796	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6694817	PI4KB	cis	parietal	SCAN
rs6694817	UBE2Q1	cis	cerebellum	SCAN
rs6694817	TDRD10	cis	lung	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
3	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
4	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr1:154393600-154402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:154393800-154402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:154393800-154403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:154394000-154404000	Weak transcription	GM12878-XiMat	blood
9	chr1:154396800-154402200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:154397000-154402200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:154397000-154402800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:154397200-154402400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:154397200-154402600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:154397200-154403800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:154398400-154403400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:154399200-154402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:154399400-154403200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:154399400-154405800	Enhancers	Right Atrium	heart
20	chr1:154399400-154407200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:154399600-154402000	Enhancers	Fetal Heart	heart
22	chr1:154399600-154402200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:154399600-154402200	Enhancers	Left Ventricle	heart
24	chr1:154399600-154402600	Enhancers	Right Ventricle	heart
25	chr1:154399600-154402800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:154399600-154403000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:154399600-154403600	Enhancers	Fetal Intestine Small	intestine
28	chr1:154399600-154403800	Enhancers	Gastric	stomach
29	chr1:154399600-154404400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr1:154399600-154404800	Enhancers	Brain Germinal Matrix	brain
31	chr1:154399600-154406800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:154399600-154409200	Enhancers	Placenta	Placenta
33	chr1:154399800-154402000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:154399800-154402400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:154399800-154402600	Enhancers	Brain Anterior Caudate	brain
36	chr1:154399800-154402600	Enhancers	Brain Hippocampus Middle	brain
37	chr1:154399800-154403000	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:154399800-154404000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:154399800-154405600	Enhancers	Fetal Intestine Large	intestine
40	chr1:154399800-154405800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:154399800-154406200	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr1:154400000-154403200	Enhancers	Brain Angular Gyrus	brain
43	chr1:154400200-154402200	Enhancers	Colon Smooth Muscle	Colon
44	chr1:154400200-154402800	Enhancers	Rectal Smooth Muscle	rectum
45	chr1:154400200-154404000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:154400400-154402000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:154400400-154402200	Enhancers	Small Intestine	intestine
48	chr1:154400400-154402800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:154400400-154402800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:154400400-154403200	Weak transcription	Placenta Amnion	Placenta Amnion

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