Variant report

Variant	rs7958241
Chromosome Location	chr12:49509262-49509263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49502659..49505990-chr12:49507842..49513633,5	MCF-7	breast:
2	chr12:49507867..49510012-chr12:49657768..49661658,4	K562	blood:
3	chr12:49454021..49456179-chr12:49508366..49510938,2	K562	blood:
4	chr12:49506528..49509640-chr12:49657775..49661658,4	K562	blood:
5	chr12:49501878..49504243-chr12:49508813..49510779,2	K562	blood:

Variant related genes	Relation type
ENSG00000139636	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1039225	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs1057548	0.83[EUR][1000 genomes]
rs10747561	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10747562	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747563	0.88[CHB][hapmap]
rs10783302	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs10783304	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783306	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783307	0.83[CEU][hapmap];0.87[ASN][1000 genomes]
rs10783308	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs10875922	0.83[ASN][1000 genomes]
rs10875924	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875925	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10875928	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10875931	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10875934	0.88[CHB][hapmap]
rs11168857	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs11168862	0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168867	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168874	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168882	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168884	0.88[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168885	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168893	0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap]
rs11168910	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap]
rs11837207	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12227296	0.83[ASN][1000 genomes]
rs12227610	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12228775	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229524	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]
rs12306494	0.84[ASN][1000 genomes]
rs12318740	0.84[ASN][1000 genomes]
rs1476137	0.88[CEU][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476138	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1874908	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs1991427	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2047101	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2162644	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2241727	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279596	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2334930	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2753	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35884657	0.81[ASN][1000 genomes]
rs3741621	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57853986	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306084	0.88[CHB][hapmap]
rs73110168	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs731350	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954521	0.88[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7954530	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7957983	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957998	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7958572	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959497	0.88[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap]
rs7969963	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969967	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976890	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7978448	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978659	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9325145	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788139	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788140	0.87[EUR][1000 genomes];0.96[ASN][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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7958241	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs7958241	DDN	cis	Muscle Skeletal	GTEx
rs7958241	TFCP2	cis	parietal	SCAN
rs7958241	C19orf55	trans	cerebellum	SCAN
rs7958241	POU6F1	cis	parietal	SCAN
rs7958241	RHEBL1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49505400-49510800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:49505400-49510800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:49505400-49511000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:49505400-49514800	Weak transcription	HSMM	muscle
5	chr12:49505400-49521000	Weak transcription	Spleen	Spleen
6	chr12:49506400-49510400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:49508400-49514800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:49508400-49515200	Weak transcription	Osteobl	bone

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