Variant report

Variant	rs6674853
Chromosome Location	chr1:154892753-154892754
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154884926..154886519-chr1:154892159..154893677,2	MCF-7	breast:
2	chr1:154892548..154895461-chr1:154971772..154973336,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1007170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796934	0.88[ASN][1000 genomes]
rs10796935	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908444	0.83[ASN][1000 genomes]
rs10908445	0.88[ASN][1000 genomes]
rs10908446	0.95[ASN][1000 genomes]
rs10908447	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109815	0.97[ASN][1000 genomes]
rs11264276	0.81[AMR][1000 genomes]
rs11264280	0.84[ASN][1000 genomes]
rs11264281	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264282	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264283	0.95[ASN][1000 genomes]
rs11264284	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264290	0.97[ASN][1000 genomes]
rs12036859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12069356	0.88[ASN][1000 genomes]
rs12095061	0.92[CEU][hapmap];0.97[ASN][1000 genomes]
rs12130132	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144978	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12406380	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1580943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976559	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977879	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061690	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2102423	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2135219	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2174507	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2335407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2335408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2335409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738026	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4240874	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4240875	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339857	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4578216	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4845398	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845399	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4845400	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845678	0.95[ASN][1000 genomes]
rs4845679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845680	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845681	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845682	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845683	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845685	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845687	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845688	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845689	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845690	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845693	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4845694	0.97[ASN][1000 genomes]
rs4845695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845696	0.97[ASN][1000 genomes]
rs58629129	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6656435	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656494	0.83[ASN][1000 genomes]
rs6669791	0.86[ASN][1000 genomes]
rs6683557	0.90[ASN][1000 genomes]
rs6686873	0.97[ASN][1000 genomes]
rs6699043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6699080	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs705094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72702224	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528532	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7544528	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7553195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs869506	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs877343	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs883718	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs906593	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9793588	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv464073	chr1:154837796-154904840	Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv547960	chr1:154837796-154904840	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv2977	chr1:154881053-154907613	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6674853	PBXIP1	Cis_1M	lymphoblastoid	RTeQTL
rs6674853	PBXIP1	cis	normal skin	skin_eQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154879200-154893200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:154879800-154894800	Weak transcription	Aorta	Aorta
3	chr1:154880400-154894400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:154881400-154894800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:154881600-154895800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:154882400-154897800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:154882800-154897400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:154883400-154894800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:154883600-154893200	Weak transcription	Liver	Liver
10	chr1:154883600-154895000	Weak transcription	Placenta	Placenta
11	chr1:154883800-154894800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:154884000-154893400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:154884000-154894600	Weak transcription	Gastric	stomach
14	chr1:154884000-154895200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:154884000-154897800	Weak transcription	HMEC	breast
16	chr1:154884600-154894800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:154884800-154894800	Weak transcription	Brain Substantia Nigra	brain
18	chr1:154884800-154894800	Weak transcription	Spleen	Spleen
19	chr1:154884800-154896200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:154884800-154908400	Weak transcription	Psoas Muscle	Psoas
21	chr1:154885000-154894800	Weak transcription	Esophagus	oesophagus
22	chr1:154885000-154895000	Weak transcription	Brain Anterior Caudate	brain
23	chr1:154885000-154895000	Weak transcription	Ovary	ovary
24	chr1:154885200-154895000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:154885400-154894800	Weak transcription	Lung	lung
26	chr1:154885600-154894200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:154885800-154893400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:154885800-154894200	Weak transcription	Fetal Brain Female	brain
29	chr1:154886000-154897200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:154886600-154894800	Weak transcription	Right Ventricle	heart
31	chr1:154886800-154894800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:154886800-154895400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:154886800-154908200	Weak transcription	Fetal Heart	heart
34	chr1:154887200-154894800	Weak transcription	Left Ventricle	heart
35	chr1:154887600-154895200	Weak transcription	NHEK	skin
36	chr1:154888000-154894800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:154888000-154894800	Weak transcription	Thymus	Thymus
38	chr1:154889600-154894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:154889600-154894800	Weak transcription	GM12878-XiMat	blood
40	chr1:154889600-154895000	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:154889600-154895000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:154889600-154897200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:154889800-154900800	Weak transcription	HepG2	liver
44	chr1:154890000-154893800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:154890000-154895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:154890000-154895000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:154890000-154896200	Weak transcription	Colonic Mucosa	Colon
48	chr1:154890200-154894800	Weak transcription	Primary B cells from cord blood	blood
49	chr1:154890400-154893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:154890400-154894600	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links