Variant report

Variant	rs10953238
Chromosome Location	chr7:97676259-97676260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11762534	1.00[ASW][hapmap];0.82[MEX][hapmap]
rs11763970	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap]
rs11764933	0.84[CEU][hapmap]
rs11765552	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs11768309	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs12670686	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12674083	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13221758	0.81[AMR][1000 genomes]
rs17435590	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs17435847	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs2132276	0.85[CEU][hapmap]
rs34249863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34307903	0.81[AMR][1000 genomes]
rs3801294	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs62477950	0.83[ASN][1000 genomes]
rs6465644	0.85[ASN][1000 genomes]
rs6465654	1.00[ASW][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs6465657	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs6465658	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap]
rs6965016	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs6967926	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap]
rs6969384	0.81[AMR][1000 genomes]
rs6977321	0.82[CEU][hapmap]
rs7804318	1.00[ASW][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap]
rs7808528	0.85[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs847580	0.81[ASN][1000 genomes]
rs989481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10953238	FIS1	cis	parietal	SCAN
rs10953238	BAIAP2L1	cis	cerebellum	SCAN
rs10953238	DKFZP434B0335	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97664000-97680400	Weak transcription	Spleen	Spleen
2	chr7:97670600-97678200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:97670800-97680400	Weak transcription	Fetal Brain Male	brain
4	chr7:97676200-97676400	Enhancers	NHEK	skin
5	chr7:97676200-97677400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:97676200-97680400	Weak transcription	Fetal Brain Female	brain

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