Variant report

Variant	rs9969217
Chromosome Location	chr7:98891438-98891439
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: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10279308	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs10953286	0.82[LWK][hapmap]
rs11771702	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11972017	0.86[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs11974885	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11976700	0.85[ASN][1000 genomes]
rs12112936	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12113440	0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12538893	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17161662	1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs17161669	1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs17161695	1.00[JPT][hapmap]
rs2003499	0.83[MEX][hapmap]
rs4729532	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs6651108	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs68164591	0.85[ASN][1000 genomes]
rs6955401	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6955490	0.88[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs6957987	0.93[ASW][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6958704	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6960805	0.82[GIH][hapmap]
rs6973408	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73395508	0.85[ASN][1000 genomes]
rs733991	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	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9969217	GS1-259H13.2	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98860600-98892800	Weak transcription	Right Atrium	heart
2	chr7:98865400-98899200	Weak transcription	Spleen	Spleen
3	chr7:98873200-98905800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:98874800-98906800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:98881200-98899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:98890000-98894400	Weak transcription	Lung	lung
7	chr7:98890400-98894200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:98890800-98892000	Enhancers	HepG2	liver
9	chr7:98890800-98905800	Weak transcription	Pancreas	Pancrea
10	chr7:98891400-98891800	Enhancers	Stomach Mucosa	stomach
11	chr7:98891400-98892000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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