Variant report

Variant	rs10908751
Chromosome Location	chr1:154187305-154187306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr1:154186892-154187318	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:154186769-154187666	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:154187122-154187313	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:154187274-154187485	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154178712..154180249-chr1:154186169..154187712,2	MCF-7	breast:
2	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
3	chr1:154179575..154184047-chr1:154184381..154189147,7	K562	blood:

Variant related genes	Relation type
C1orf43	TF binding region
ENSG00000163263	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10797058	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10797061	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908739	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11265285	0.89[EUR][1000 genomes]
rs1194580	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]
rs1194582	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194599	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194603	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];0.88[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1194604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044616	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063830	1.00[ASW][hapmap];0.87[GIH][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12095767	0.84[AMR][1000 genomes];0.93[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790686	0.82[CHB][hapmap]
rs2841108	0.82[CHB][hapmap]
rs3001365	0.82[CHB][hapmap]
rs4072431	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364874	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579747	1.00[ASW][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845364	0.86[ASW][hapmap]
rs4845605	1.00[ASW][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap]
rs4845609	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.82[EUR][1000 genomes]
rs7516809	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7526644	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533952	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9803862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804045	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10908751	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154172200-154190000	Weak transcription	Fetal Heart	heart
2	chr1:154177000-154191000	Strong transcription	Fetal Stomach	stomach
3	chr1:154177000-154192000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:154177200-154187400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:154177200-154187600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:154177200-154190200	Strong transcription	Primary T cells from cord blood	blood
7	chr1:154177400-154190400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:154177600-154187400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:154177600-154187400	Strong transcription	Fetal Thymus	thymus
10	chr1:154177600-154191400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:154177800-154187400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:154177800-154187400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:154177800-154187400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:154177800-154187400	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:154177800-154187400	Strong transcription	Fetal Intestine Large	intestine
16	chr1:154177800-154187600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:154177800-154188000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:154177800-154190400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:154177800-154190600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:154177800-154190600	Strong transcription	Fetal Intestine Small	intestine
21	chr1:154177800-154191000	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:154177800-154191400	Strong transcription	Placenta	Placenta
23	chr1:154178000-154189800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:154178200-154189200	Strong transcription	Lung	lung
25	chr1:154178200-154191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:154178400-154187400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:154178400-154187400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:154178400-154187400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:154178400-154187400	Strong transcription	Dnd41	blood
30	chr1:154178400-154187600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:154178400-154187600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:154178600-154187400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:154178600-154187400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:154178600-154187600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:154178600-154188000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:154178800-154187400	Strong transcription	Thymus	Thymus
37	chr1:154178800-154187600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:154178800-154188000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:154179400-154191000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:154180000-154191000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:154180200-154190800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:154182400-154187400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:154183000-154187600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:154183000-154188000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:154183800-154191000	Weak transcription	Right Atrium	heart
46	chr1:154184200-154187400	Strong transcription	GM12878-XiMat	blood
47	chr1:154184600-154187600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:154185200-154190000	Weak transcription	Esophagus	oesophagus
49	chr1:154185200-154192000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:154185600-154187400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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