Variant report

Variant	rs1194580
Chromosome Location	chr1:154219485-154219486
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154219361..154222191-chr1:154229883..154232153,2	K562	blood:
2	chr1:154211935..154214762-chr1:154216563..154219811,3	MCF-7	breast:
3	chr1:154191702..154193610-chr1:154219439..154221182,2	K562	blood:
4	chr1:154211340..154215843-chr1:154217850..154221310,6	K562	blood:
5	chr1:154154425..154156684-chr1:154218520..154221156,2	MCF-7	breast:
6	chr1:154210658..154214803-chr1:154216327..154221110,6	K562	blood:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10797058	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10797061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908739	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908751	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265285	0.87[EUR][1000 genomes]
rs1194582	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194596	0.80[GIH][hapmap]
rs1194599	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194604	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];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044616	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063830	1.00[ASW][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12095767	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12354278	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13796	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1591902	1.00[CHB][hapmap]
rs1832582	1.00[JPT][hapmap]
rs2220390	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];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2340473	0.81[GIH][hapmap]
rs2790686	0.82[CHB][hapmap]
rs4072431	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364874	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4393149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579747	1.00[ASW][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845364	0.86[ASW][hapmap]
rs4845605	1.00[ASW][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs4845609	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807361	0.85[ASN][1000 genomes]
rs6667222	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6680947	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6719	0.81[GIH][hapmap]
rs7516809	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7526644	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9803857	0.81[GIH][hapmap]
rs9803862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804045	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943097	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1194580	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL
rs1194580	C1orf43	cis	parietal	SCAN
rs1194580	CKS1B	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154195400-154234600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:154196600-154237600	Strong transcription	Fetal Thymus	thymus
6	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:154196800-154224200	Strong transcription	K562	blood
8	chr1:154196800-154224400	Strong transcription	Primary B cells from cord blood	blood
9	chr1:154196800-154235800	Strong transcription	HUVEC	blood vessel
10	chr1:154196800-154242600	Strong transcription	A549	lung
11	chr1:154197000-154235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:154197400-154224200	Strong transcription	Hela-S3	cervix
20	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
21	chr1:154197600-154226400	Strong transcription	Osteobl	bone
22	chr1:154197600-154236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:154197600-154236200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:154197600-154236800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:154197600-154239200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:154197600-154239200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:154197600-154239400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:154197600-154239800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:154197600-154239800	Strong transcription	NHLF	lung
30	chr1:154197600-154242000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
36	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
37	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:154197800-154220400	Strong transcription	Primary T cells from cord blood	blood
39	chr1:154197800-154236400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:154197800-154237200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:154197800-154239600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:154197800-154242000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
45	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:154198000-154219600	Strong transcription	Brain Germinal Matrix	brain
47	chr1:154198000-154243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:154198200-154241000	Strong transcription	Dnd41	blood
50	chr1:154198400-154236600	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links