Variant report

Variant	rs733991
Chromosome Location	chr7:98895250-98895251
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	POLR2A	chr7:98890111-98895513	K562	blood:	n/a	n/a

Variant related genes	Relation type
MYH16	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10155966	0.83[CEU][hapmap]
rs10225529	0.89[EUR][1000 genomes]
rs10243678	0.83[CEU][hapmap]
rs10258757	0.83[CEU][hapmap]
rs10267346	0.85[EUR][1000 genomes]
rs10270459	0.83[CEU][hapmap]
rs10270917	0.83[CEU][hapmap]
rs10272998	0.83[CEU][hapmap]
rs10279308	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs11762273	0.83[CEU][hapmap]
rs11771702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972017	0.82[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap]
rs11974885	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11976700	0.89[ASN][1000 genomes]
rs11977673	1.00[CHB][hapmap]
rs11978089	0.91[CEU][hapmap]
rs12112936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538893	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17161662	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161669	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs17161695	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2003499	0.91[CEU][hapmap];0.83[MEX][hapmap]
rs2072181	0.83[CEU][hapmap]
rs2286162	0.83[CEU][hapmap]
rs3801288	0.83[CEU][hapmap]
rs4729532	0.91[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs59131705	0.90[ASN][1000 genomes]
rs6651108	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs68164591	1.00[ASN][1000 genomes]
rs6943920	0.83[CEU][hapmap]
rs6955401	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6955490	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6957987	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958704	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960805	0.82[GIH][hapmap]
rs6973408	0.81[CEU][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395508	1.00[ASN][1000 genomes]
rs9768020	0.85[EUR][1000 genomes]
rs9969217	0.92[ASW][hapmap];0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9969386	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs733991	GS1-259H13.2	cis	Thyroid	GTEx
rs733991	GATS	cis	parietal	SCAN
rs733991	CPSF4	cis	parietal	SCAN
rs733991	ZKSCAN1	cis	parietal	SCAN
rs733991	OR2AE1	cis	parietal	SCAN
rs733991	STAG3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98865400-98899200	Weak transcription	Spleen	Spleen
2	chr7:98873200-98905800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:98874800-98906800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:98881200-98899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:98890800-98905800	Weak transcription	Pancreas	Pancrea
6	chr7:98893200-98906600	Weak transcription	Fetal Intestine Small	intestine
7	chr7:98893800-98906000	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links