Variant report

Variant	rs11787888
Chromosome Location	chr9:95993326-95993327
allele	C/T
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	EP300	chr9:95993136-95994064	ECC-1	luminal epithelium:	n/a	n/a
2	ZBTB7A	chr9:95993286-95994124	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr9:95993322-95994182	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr9:95993083-95994177	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr9:95993175-95994182	ECC-1	luminal epithelium:	n/a	chr9:95994080-95994090 chr9:95994083-95994093 chr9:95994144-95994151 chr9:95994084-95994091 chr9:95993643-95993653
6	EP300	chr9:95993238-95993819	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr9:95993072-95994120	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr9:95993198-95994141	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr9:95993256-95994342	ECC-1	luminal epithelium:	n/a	chr9:95994080-95994090 chr9:95994083-95994093 chr9:95994144-95994151 chr9:95994084-95994091 chr9:95993643-95993653
10	POLR2A	chr9:95993296-95994157	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95895055..95896953-chr9:95991458..95994439,3	MCF-7	breast:
2	chr9:95992848..95994419-chr9:95997812..96000158,2	MCF-7	breast:
3	chr9:95985503..95987734-chr9:95991883..95994859,2	K562	blood:
4	chr9:95959322..95962228-chr9:95991755..95995134,3	MCF-7	breast:
5	chr9:95896382..95898077-chr9:95992649..95994936,2	MCF-7	breast:

Variant related genes	Relation type
WNK2	TF binding region
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10992681	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]
rs10992699	0.82[AMR][1000 genomes]
rs1107614	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1107615	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11790795	0.82[AMR][1000 genomes]
rs11793893	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11794044	0.82[AMR][1000 genomes]
rs12000967	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12001073	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12002458	0.87[AMR][1000 genomes]
rs12005950	0.82[AMR][1000 genomes]
rs13283550	0.82[AMR][1000 genomes]
rs13287544	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13290796	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]
rs13296817	0.84[TSI][hapmap]
rs13301530	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1936399	0.82[AMR][1000 genomes]
rs34020099	0.82[AMR][1000 genomes]
rs34085543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34834050	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35199621	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35305079	0.80[AMR][1000 genomes]
rs35438673	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35438843	0.82[AMR][1000 genomes]
rs35712744	0.80[AMR][1000 genomes]
rs4329328	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4744213	0.85[MEX][hapmap]
rs55981123	0.83[AMR][1000 genomes]
rs6479471	0.96[TSI][hapmap];0.82[AMR][1000 genomes]
rs6479474	1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7019910	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7022051	1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7031721	0.82[AMR][1000 genomes]
rs7042943	1.00[MEX][hapmap];0.96[TSI][hapmap]
rs7046965	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7848843	0.82[AMR][1000 genomes]
rs7855391	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7857220	0.85[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7867954	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7873162	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7874101	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7875384	0.85[MEX][hapmap]

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
rs11787888	SECISBP2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95984800-95998000	Enhancers	Pancreas	Pancrea
2	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:95987200-95996800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:95987200-95997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:95987200-96000200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:95987400-95994800	Weak transcription	Psoas Muscle	Psoas
7	chr9:95987400-95995000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:95988200-95993400	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
12	chr9:95988400-95999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:95988600-95997200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:95990400-95994000	Enhancers	Fetal Heart	heart
15	chr9:95990400-95994000	Enhancers	Right Ventricle	heart
16	chr9:95990800-95995000	Enhancers	Colonic Mucosa	Colon
17	chr9:95991200-95994800	Strong transcription	HepG2	liver
18	chr9:95991200-95995200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr9:95992200-95993400	Weak transcription	Left Ventricle	heart
20	chr9:95992200-95993400	Weak transcription	Spleen	Spleen
21	chr9:95992200-95993600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:95992200-95995200	Enhancers	Stomach Mucosa	stomach
23	chr9:95992200-95999800	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:95992400-95993400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:95992400-95993600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr9:95992400-95994200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:95992400-95994400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:95992600-95993600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr9:95992600-95994400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr9:95992600-95994400	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr9:95992600-95995200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr9:95992800-95993600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:95992800-95993800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr9:95992800-95993800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
35	chr9:95992800-95994000	Genic enhancers	Brain Germinal Matrix	brain
36	chr9:95992800-95994000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:95992800-95994600	Enhancers	Gastric	stomach
38	chr9:95993000-95994000	Genic enhancers	Fetal Brain Female	brain
39	chr9:95993000-95995000	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr9:95993200-95993400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr9:95993200-95993600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:95993200-95993600	Flanking Active TSS	Fetal Intestine Large	intestine
43	chr9:95993200-95993600	Enhancers	Fetal Lung	lung
44	chr9:95993200-95993800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:95993200-95993800	Enhancers	Small Intestine	intestine
46	chr9:95993200-95994200	Enhancers	Brain Anterior Caudate	brain
47	chr9:95993200-95994600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:95993200-95995000	Bivalent Enhancer	Fetal Stomach	stomach

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