Variant report

Variant	rs4658273
Chromosome Location	chr1:92274308-92274309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92274050..92276390-chr1:92277677..92279989,2	K562	blood:
2	chr1:92274046..92275550-chr1:92277677..92280459,2	K562	blood:
3	chr1:92269279..92272009-chr1:92273334..92276001,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10493859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11165546	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11466567	0.81[AFR][1000 genomes]
rs11578569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11804539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12118714	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12123363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134037	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12751910	1.00[CHB][hapmap]
rs1556192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17443164	1.00[CHB][hapmap]
rs17515100	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2046738	0.89[AMR][1000 genomes]
rs2489179	0.90[AMR][1000 genomes]
rs2489183	0.80[AMR][1000 genomes]
rs2810884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2996482	0.86[AMR][1000 genomes]
rs4658269	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs4658270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs4658274	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6604053	1.00[CHB][hapmap]
rs71650466	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription 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 lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4658273	C1orf146	cis	parietal	SCAN
rs4658273	GFI1	cis	parietal	SCAN
rs4658273	HSP90B3P	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92257600-92279400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:92262800-92277000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:92264800-92284200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:92266800-92277400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:92268200-92274600	Enhancers	Placenta	Placenta
6	chr1:92268600-92275200	Enhancers	NHDF-Ad	bronchial
7	chr1:92268600-92275800	Enhancers	Pancreas	Pancrea
8	chr1:92269400-92275600	Enhancers	Fetal Heart	heart
9	chr1:92269600-92275800	Enhancers	Left Ventricle	heart
10	chr1:92270000-92278000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:92270200-92274800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:92270200-92276800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:92270400-92274800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:92270400-92274800	Weak transcription	HSMM	muscle
15	chr1:92270400-92275600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:92270400-92277600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:92270600-92274800	Weak transcription	Esophagus	oesophagus
18	chr1:92271200-92274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:92271200-92276200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:92271400-92274600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:92271400-92274800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:92271400-92274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:92271400-92275000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:92271400-92276000	Weak transcription	Primary T cells from cord blood	blood
25	chr1:92271600-92274600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:92271600-92274600	Weak transcription	GM12878-XiMat	blood
27	chr1:92271600-92274800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:92271600-92274800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:92271800-92275600	Enhancers	HUVEC	blood vessel
30	chr1:92272000-92274600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:92272000-92279200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:92272200-92282600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:92272400-92285400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:92272600-92274600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:92273000-92274800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:92273000-92277400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:92273000-92277400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:92273200-92275400	Weak transcription	Fetal Stomach	stomach
39	chr1:92273200-92277400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:92273400-92274400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:92273400-92274400	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:92273400-92274600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:92273400-92274600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:92273400-92274600	Weak transcription	HepG2	liver
45	chr1:92273400-92274600	Weak transcription	Osteobl	bone
46	chr1:92273400-92274800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:92273400-92274800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:92273400-92274800	Weak transcription	Adipose Nuclei	Adipose
49	chr1:92273400-92274800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:92273400-92274800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links