Variant report

Variant	rs1933680
Chromosome Location	chr9:96709483-96709484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96705963..96707541-chr9:96709329..96711419,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1057713	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10821273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11788035	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11789015	0.82[ASW][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs11792744	0.82[YRI][hapmap]
rs11999521	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11999551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12005806	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1320546	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13283836	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13291289	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1933681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933682	0.82[AMR][1000 genomes]
rs2095778	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35001304	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4437716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4563951	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56285369	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7034685	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858520	0.86[AFR][1000 genomes]
rs7872123	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1035418	chr9:96647940-96711409	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1933680	SPTLC1	cis	cerebellum	SCAN
rs1933680	IPPK	cis	parietal	SCAN
rs1933680	ORMDL2	trans	parietal	SCAN
rs1933680	WNK2	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96708600-96710600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:96708600-96713000	Weak transcription	Gastric	stomach
3	chr9:96708800-96710000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr9:96708800-96710400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr9:96708800-96710400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr9:96709000-96709600	Enhancers	Stomach Smooth Muscle	stomach
7	chr9:96709000-96713200	Weak transcription	Right Atrium	heart
8	chr9:96709200-96709800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
9	chr9:96709200-96710800	Weak transcription	Pancreas	Pancrea
10	chr9:96709400-96710000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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