Variant report

Variant	rs10992681
Chromosome Location	chr9:95978265-95978266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:46012490..46013452-chr9:95977787..95978369,2	MCF-7	breast:
2	chr9:95962951..95965584-chr9:95975622..95978516,3	MCF-7	breast:
3	chr9:95965438..95972862-chr9:95973191..95979158,8	MCF-7	breast:
4	chr9:95976952..95979660-chr9:95981802..95984086,2	MCF-7	breast:
5	chr9:95977876..95978624-chr9:96064689..96065566,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1107614	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1107615	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11787888	1.00[ASW][hapmap];1.00[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];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790795	0.87[AMR][1000 genomes]
rs11793893	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11794044	0.87[AMR][1000 genomes]
rs12001073	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12002458	0.82[AMR][1000 genomes]
rs13287544	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13290796	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13301530	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1936399	0.87[AMR][1000 genomes]
rs34020099	0.87[AMR][1000 genomes]
rs34085543	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34834050	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35199621	0.82[AMR][1000 genomes]
rs35305079	0.85[AMR][1000 genomes]
rs35438673	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35438843	0.87[AMR][1000 genomes]
rs35712744	0.85[AMR][1000 genomes]
rs36101213	0.81[AMR][1000 genomes]
rs4329328	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744213	0.85[MEX][hapmap]
rs6479471	0.92[TSI][hapmap]
rs6479474	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs7019910	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022051	1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs7031721	0.87[AMR][1000 genomes]
rs7042943	1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7046965	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7855391	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7857220	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7867954	0.82[AMR][1000 genomes]
rs7873162	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7874101	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7875384	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv614880	chr9:95930572-95978265	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992681	SECISBP2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95955800-95985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:95971000-95979800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:95971000-95979800	Weak transcription	Small Intestine	intestine
4	chr9:95971000-95981400	Weak transcription	Brain Hippocampus Middle	brain
5	chr9:95971200-95985800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:95971600-95979600	Weak transcription	Spleen	Spleen
7	chr9:95972800-95979600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:95973000-95979600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr9:95974200-95985400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:95974400-95986800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:95975000-95979800	Weak transcription	Gastric	stomach
12	chr9:95975400-95979600	Weak transcription	HepG2	liver
13	chr9:95975400-95979800	Weak transcription	Psoas Muscle	Psoas
14	chr9:95975600-95979400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:95975600-95979600	Weak transcription	Left Ventricle	heart
16	chr9:95975600-95979600	Weak transcription	Pancreas	Pancrea
17	chr9:95975600-95979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:95975600-95979800	Weak transcription	Right Ventricle	heart
19	chr9:95975600-95979800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:95976400-95979600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:95977400-95978600	Weak transcription	Colonic Mucosa	Colon
22	chr9:95978200-95978600	Enhancers	Fetal Heart	heart

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