Variant report

Variant	rs1391558
Chromosome Location	chr1:222848029-222848030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222846053..222848100-chr1:222867819..222869490,2	K562	blood:
2	chr1:222845342..222848265-chr1:222850584..222852814,2	K562	blood:
3	chr1:222836136..222838189-chr1:222847780..222849818,2	MCF-7	breast:
4	chr1:222815720..222818727-chr1:222847963..222850560,3	K562	blood:

Variant related genes	Relation type
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11485123	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12063226	0.85[EUR][1000 genomes]
rs1391557	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1498382	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17011666	0.95[MEX][hapmap]
rs17011686	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs17163337	0.81[JPT][hapmap]
rs17163450	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs17163468	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs1909197	0.82[EUR][1000 genomes]
rs2030076	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2088514	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2133188	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2270707	1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs2378604	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936020	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2936023	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2936049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936051	0.92[EUR][1000 genomes]
rs2936052	0.92[EUR][1000 genomes]
rs2936054	0.91[EUR][1000 genomes]
rs3002129	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002146	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3002148	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3008614	0.91[EUR][1000 genomes]
rs3008615	0.91[EUR][1000 genomes]
rs3008616	0.91[EUR][1000 genomes]
rs3008618	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3008622	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008625	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3008629	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3008637	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34433664	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35507977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3811465	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61827168	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6683071	0.80[ASW][hapmap]

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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription 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	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1391558	C1orf58	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222836600-222849600	Weak transcription	Stomach Mucosa	stomach
3	chr1:222839000-222849000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:222839000-222849000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:222839000-222854400	Weak transcription	Lung	lung
6	chr1:222839000-222859800	Weak transcription	Small Intestine	intestine
7	chr1:222839000-222877400	Weak transcription	Psoas Muscle	Psoas
8	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:222839200-222861200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
11	chr1:222839800-222848800	Weak transcription	Right Ventricle	heart
12	chr1:222839800-222859600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:222839800-222859600	Weak transcription	Fetal Brain Male	brain
14	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
15	chr1:222841000-222859600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:222841200-222866200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:222841200-222883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:222841400-222848800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:222841400-222883200	Weak transcription	Fetal Heart	heart
20	chr1:222842600-222850000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:222842600-222850000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:222842800-222849600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:222842800-222849800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:222842800-222867800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:222843200-222849200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:222843200-222849200	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr1:222843200-222849400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:222843200-222849400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:222843200-222849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:222843200-222849800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:222843200-222849800	Strong transcription	Osteobl	bone
32	chr1:222843200-222850200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:222843200-222850600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:222843200-222850800	Strong transcription	NH-A	brain
35	chr1:222843400-222848800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:222843400-222849200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:222843400-222849200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:222843400-222849200	Strong transcription	HMEC	breast
39	chr1:222843400-222849400	Strong transcription	Adipose Nuclei	Adipose
40	chr1:222843400-222849400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:222843400-222849600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:222843400-222849800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:222843400-222849800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:222843400-222849800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:222843400-222849800	Strong transcription	Placenta	Placenta
46	chr1:222843400-222850400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:222843400-222851000	Strong transcription	Primary B cells from cord blood	blood
48	chr1:222843400-222860200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:222843600-222849600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:222843600-222849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links