Variant report

Variant	rs13290796
Chromosome Location	chr9:95991547-95991548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95989727..95992528-chr9:95997784..96000690,3	MCF-7	breast:
2	chr9:95990183..95991762-chr9:95997041..95999107,2	K562	blood:
3	chr9:95895055..95896953-chr9:95991458..95994439,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10992681	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]
rs1107614	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107615	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787888	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11793893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002458	0.83[AMR][1000 genomes]
rs13287544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34085543	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34834050	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35199621	0.83[AMR][1000 genomes]
rs35438673	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329328	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479471	0.92[TSI][hapmap]
rs6479474	0.85[MEX][hapmap];0.87[TSI][hapmap]
rs7019910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022051	0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs7042943	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7046965	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857220	0.92[TSI][hapmap]
rs7867954	0.83[AMR][1000 genomes]
rs7873162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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
rs13290796	SECISBP2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95979600-95992200	Enhancers	Left Ventricle	heart
2	chr9:95984800-95998000	Enhancers	Pancreas	Pancrea
3	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:95987200-95992000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:95987200-95996800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:95987200-95997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:95987200-96000200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:95987400-95991800	Weak transcription	Spleen	Spleen
9	chr9:95987400-95992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:95987400-95992600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:95987400-95992800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:95987400-95994800	Weak transcription	Psoas Muscle	Psoas
13	chr9:95987400-95995000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:95988200-95991600	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:95988200-95992200	Weak transcription	Fetal Brain Female	brain
18	chr9:95988200-95993200	Weak transcription	Brain Anterior Caudate	brain
19	chr9:95988200-95993200	Enhancers	Fetal Intestine Large	intestine
20	chr9:95988200-95993400	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
22	chr9:95988400-95992800	Genic enhancers	Fetal Intestine Small	intestine
23	chr9:95988400-95999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:95988600-95997200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:95990200-95991800	Enhancers	Stomach Mucosa	stomach
26	chr9:95990400-95992200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr9:95990400-95992800	Enhancers	Duodenum Mucosa	Duodenum
28	chr9:95990400-95992800	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr9:95990400-95992800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr9:95990400-95994000	Enhancers	Fetal Heart	heart
31	chr9:95990400-95994000	Enhancers	Right Ventricle	heart
32	chr9:95990800-95991600	Enhancers	Stomach Smooth Muscle	stomach
33	chr9:95990800-95991800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:95990800-95995000	Enhancers	Colonic Mucosa	Colon
35	chr9:95991000-95993200	Weak transcription	Small Intestine	intestine
36	chr9:95991200-95991800	Weak transcription	Right Atrium	heart
37	chr9:95991200-95992200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:95991200-95992600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:95991200-95992800	Weak transcription	Gastric	stomach
40	chr9:95991200-95994800	Strong transcription	HepG2	liver
41	chr9:95991200-95995200	Enhancers	Skeletal Muscle Female	skeletal muscle

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