Variant report

Variant	rs1251484
Chromosome Location	chr1:76504146-76504147
allele	A/G
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	TEAD4	chr1:76504024-76504371	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr1:76503955-76504533	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr1:76503821-76504504	SK-N-SH	brain:	n/a	n/a
4	JUND	chr1:76503856-76504503	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr1:76503839-76504387	SK-N-SH	brain:	n/a	n/a
6	JUND	chr1:76503733-76504442	SK-N-SH	brain:	n/a	n/a
7	MAFK	chr1:76504013-76504198	HepG2	liver:	n/a	chr1:76504095-76504111 chr1:76504095-76504106 chr1:76504095-76504106 chr1:76504094-76504108 chr1:76504096-76504107
8	EP300	chr1:76503933-76504309	SK-N-SH_RA	brain:	n/a	chr1:76503992-76504006
9	POLR2A	chr1:76503946-76504329	SK-N-MC	brain:	n/a	n/a
10	PBX3	chr1:76503823-76504471	SK-N-SH	brain:	n/a	n/a
11	MAX	chr1:76503926-76504320	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr1:76503754-76504505	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr1:76503941-76504358	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr1:76503857-76504539	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr1:76503688-76504539	SK-N-SH	brain:	n/a	chr1:76504068-76504077 chr1:76504066-76504079 chr1:76504066-76504078 chr1:76504068-76504075 chr1:76504064-76504080 chr1:76504067-76504077
16	POLR2A	chr1:76503857-76504382	SK-N-SH	brain:	n/a	n/a
17	TCF12	chr1:76503809-76504549	SK-N-SH	brain:	n/a	n/a
18	EP300	chr1:76503721-76504518	SK-N-SH	brain:	n/a	chr1:76503992-76504006
19	EP300	chr1:76504005-76504284	SK-N-SH_RA	brain:	n/a	n/a
20	GATA3	chr1:76503581-76504588	SK-N-SH	brain:	n/a	chr1:76504068-76504077 chr1:76504066-76504079 chr1:76504066-76504078 chr1:76504068-76504075 chr1:76504064-76504080 chr1:76504067-76504077

Variant related genes	Relation type
ENSG00000230027	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10782605	0.84[EUR][1000 genomes]
rs10873865	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123144	0.91[CEU][hapmap]
rs12123760	0.91[CEU][hapmap]
rs12125940	0.87[EUR][1000 genomes]
rs12126074	0.87[EUR][1000 genomes]
rs12145522	0.87[EUR][1000 genomes]
rs1251476	0.88[AFR][1000 genomes]
rs1251485	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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251486	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251489	0.89[EUR][1000 genomes]
rs1251492	0.90[EUR][1000 genomes]
rs1251494	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251495	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251496	0.90[EUR][1000 genomes]
rs1251501	0.90[EUR][1000 genomes]
rs1251502	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1251504	0.90[EUR][1000 genomes]
rs1251505	0.90[EUR][1000 genomes]
rs1251506	0.89[EUR][1000 genomes]
rs1251507	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1251509	0.89[EUR][1000 genomes]
rs1251510	0.88[EUR][1000 genomes]
rs1251511	0.90[EUR][1000 genomes]
rs1251512	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251513	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1251519	0.84[AFR][1000 genomes]
rs1251526	0.84[AFR][1000 genomes]
rs1251528	0.84[AFR][1000 genomes]
rs1266117	0.90[EUR][1000 genomes]
rs1340690	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1340691	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17607383	0.89[EUR][1000 genomes]
rs17659615	0.89[EUR][1000 genomes]
rs1770895	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34354538	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35318380	0.87[EUR][1000 genomes]
rs35381129	0.87[EUR][1000 genomes]
rs5022490	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60182743	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1251484	SNORD45B	cis	cerebellum	SCAN
rs1251484	ACADM	cis	cerebellum	SCAN
rs1251484	MSH4	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76501800-76504200	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr1:76501800-76504400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
4	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
5	chr1:76502800-76504200	Enhancers	Stomach Mucosa	stomach
6	chr1:76503000-76504200	Enhancers	Fetal Stomach	stomach
7	chr1:76503000-76504400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:76503000-76504800	Enhancers	Fetal Kidney	kidney
9	chr1:76503000-76505200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:76503200-76504200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:76503200-76504200	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr1:76503200-76504400	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:76503200-76505000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:76503400-76504200	Enhancers	Fetal Lung	lung
15	chr1:76503400-76505200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:76503400-76505800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:76503400-76505800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:76503400-76507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:76503600-76504200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:76503600-76504800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:76503600-76505800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:76503600-76509600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:76503800-76504200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr1:76503800-76504200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:76503800-76504200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:76504000-76504200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:76504000-76505000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:76504000-76505200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:76504000-76509200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links