Variant report

Variant	rs750052
Chromosome Location	chr15:42361022-42361023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42359873..42362452-chr15:42410836..42413040,2	K562	blood:
2	chr15:42360775..42361464-chr15:42423274..42423858,2	MCF-7	breast:
3	chr15:42360949..42362087-chr15:42429641..42430534,4	MCF-7	breast:
4	chr15:42352029..42354148-chr15:42359763..42361344,2	K562	blood:
5	chr15:42360712..42361732-chr15:42376391..42377254,4	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11070356	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12148273	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17690109	0.91[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17690827	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17690899	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17691153	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17747505	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17748059	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17748132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1993069	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2412656	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28568280	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3743017	1.00[ASW][hapmap]
rs4923922	0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4923923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923924	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923925	0.99[EUR][1000 genomes]
rs4923926	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923927	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923928	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924608	1.00[ASW][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs4924609	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4924611	0.92[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924614	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4924615	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4924616	0.99[EUR][1000 genomes]
rs4924617	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4924619	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924620	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7162019	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7165458	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7165460	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7166026	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7166093	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7166111	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7166789	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7168863	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173686	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7176443	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176459	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7177034	0.82[CEU][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7180420	0.99[EUR][1000 genomes]
rs750051	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs755599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8029713	1.00[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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 miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs750052	RTF1	cis	parietal	SCAN
rs750052	IVD	cis	parietal	SCAN
rs750052	FAM98B	cis	parietal	SCAN
rs750052	GPR176	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42350400-42362600	Weak transcription	Gastric	stomach
2	chr15:42358200-42363000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:42358400-42361600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:42360400-42361400	Enhancers	HSMMtube	muscle
5	chr15:42360400-42363600	Enhancers	Fetal Muscle Leg	muscle
6	chr15:42360600-42362800	Enhancers	Fetal Muscle Trunk	muscle
7	chr15:42360800-42362800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:42360800-42363400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:42361000-42363400	Weak transcription	Esophagus	oesophagus

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