Variant report

Variant	rs11042725
Chromosome Location	chr11:10325325-10325326
allele	A/C
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	CEBPB	chr11:10323999-10327509	Hela-S3	cervix:	n/a	chr11:10325931-10325943
2	TCF7L2	chr11:10323887-10325849	Hela-S3	cervix:	n/a	n/a
3	KAP1	chr11:10323569-10326338	HEK293	kidney:	n/a	n/a
4	TAF1	chr11:10325256-10325758	Hela-S3	cervix:	n/a	n/a
5	JUND	chr11:10323956-10331669	HCT-116	colon:	n/a	chr11:10326447-10326456 chr11:10331225-10331234 chr11:10326563-10326572 chr11:10331227-10331234 chr11:10324905-10324915 chr11:10329473-10329484 chr11:10331226-10331235 chr11:10329705-10329717 chr11:10329705-10329716 chr11:10331226-10331234 chr11:10329706-10329716 chr11:10330671-10330679 chr11:10329707-10329715 chr11:10329706-10329716 chr11:10329706-10329716 chr11:10331224-10331235
6	NFIC	chr11:10323716-10326756	ECC-1	luminal epithelium:	n/a	n/a
7	TAF7	chr11:10324386-10331444	H1-hESC	embryonic stem cell:	n/a	n/a
8	RUNX3	chr11:10325105-10325656	GM12878	blood:	n/a	n/a
9	YY1	chr11:10324344-10325578	ECC-1	luminal epithelium:	n/a	chr11:10325060-10325071 chr11:10324358-10324369 chr11:10324943-10324955
10	CTCF	chr11:10323213-10327582	A549	lung:	n/a	n/a
11	CHD2	chr11:10324029-10327973	Hela-S3	cervix:	n/a	chr11:10327760-10327770 chr11:10327860-10327870 chr11:10326455-10326465 chr11:10326448-10326458
12	REST	chr11:10323825-10327134	A549	lung:	n/a	chr11:10324706-10324726 chr11:10324706-10324726 chr11:10324841-10324861 chr11:10324470-10324483 chr11:10324706-10324726 chr11:10324845-10324858 chr11:10324707-10324725
13	POLR2A	chr11:10324106-10328040	HepG2	liver:	n/a	n/a
14	FOS	chr11:10325301-10325962	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr11:10324941-10325376	A549	lung:	n/a	n/a
16	CTCF	chr11:10325200-10325350	Caco-2	colon:	n/a	n/a
17	BCL3	chr11:10325122-10326074	A549	lung:	n/a	n/a
18	CEBPB	chr11:10325087-10326873	A549	lung:	n/a	chr11:10325931-10325943
19	POLR2A	chr11:10325037-10325899	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr11:10324943-10325808	A549	lung:	n/a	n/a
21	POLR2A	chr11:10324517-10325861	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr11:10323526-10327709	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr11:10325194-10327128	Hela-S3	cervix:	n/a	chr11:10326951-10326963 chr11:10326172-10326182
24	TEAD4	chr11:10325253-10325900	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr11:10324139-10325847	HepG2	liver:	n/a	n/a
26	SMC3	chr11:10323716-10327728	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr11:10325280-10325430	GM12873	blood:	n/a	n/a
28	SRF	chr11:10325246-10326796	ECC-1	luminal epithelium:	n/a	chr11:10325856-10325869 chr11:10325854-10325871 chr11:10325857-10325871 chr11:10325858-10325869 chr11:10325854-10325868 chr11:10326120-10326130 chr11:10325855-10325870 chr11:10325857-10325868 chr11:10325852-10325870 chr11:10325856-10325869 chr11:10325858-10325867 chr11:10325356-10325370 chr11:10325856-10325867
29	POLR2A	chr11:10323851-10331424	HCT-116	colon:	n/a	n/a
30	CHD1	chr11:10324427-10326303	H1-hESC	embryonic stem cell:	n/a	n/a
31	RCOR1	chr11:10323888-10327369	Hela-S3	cervix:	n/a	n/a
32	BCL3	chr11:10325110-10326980	A549	lung:	n/a	chr11:10326199-10326207 chr11:10326562-10326575 chr11:10326567-10326580
33	FOSL2	chr11:10324535-10325997	A549	lung:	n/a	chr11:10324905-10324915
34	POLR2A	chr11:10324418-10325850	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:10323816-10331549	Hela-S3	cervix:	n/a	n/a
36	BACH1	chr11:10325267-10326939	H1-hESC	embryonic stem cell:	n/a	n/a
37	FOS	chr11:10325306-10325923	MCF10A-Er-Src	breast:	n/a	n/a
38	RAD21	chr11:10324040-10327869	IMR90	lung:	n/a	chr11:10326951-10326963 chr11:10326172-10326182
39	MAX	chr11:10324249-10325821	NB4	blood:	n/a	chr11:10325336-10325345 chr11:10324414-10324425
40	FOS	chr11:10325324-10325952	MCF10A-Er-Src	breast:	n/a	n/a
41	MTA3	chr11:10325157-10325954	GM12878	blood:	n/a	n/a
42	RCOR1	chr11:10325314-10325708	K562	blood:	n/a	n/a
43	SIN3AK20	chr11:10323807-10331742	HCT-116	colon:	n/a	n/a
44	POLR2A	chr11:10324111-10325931	ECC-1	luminal epithelium:	n/a	n/a
45	ELK4	chr11:10324899-10325794	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr11:10324077-10325828	A549	lung:	n/a	n/a
47	MAX	chr11:10323478-10330100	A549	lung:	n/a	chr11:10329125-10329138 chr11:10325336-10325345 chr11:10329127-10329134 chr11:10329125-10329138 chr11:10329125-10329138 chr11:10326516-10326525 chr11:10329353-10329363 chr11:10329122-10329141 chr11:10327866-10327876 chr11:10324414-10324425
48	POLR2A	chr11:10324280-10325942	HCT-116	colon:	n/a	n/a
49	POLR2A	chr11:10323780-10328609	Hela-S3	cervix:	n/a	n/a
50	CHD1	chr11:10322517-10331634	IMR90	lung:	n/a	chr11:10327760-10327770 chr11:10327860-10327870 chr11:10326455-10326465 chr11:10326448-10326458

No.	Distal block	Cell Line	Cell type
1	chr11:10324179..10326085-chr11:10337865..10340352,2	MCF-7	breast:
2	chr11:10314668..10317041-chr11:10325018..10327085,3	K562	blood:
3	chr11:10322610..10325546-chr11:10673380..10676333,2	K562	blood:
4	chr11:10325145..10326103-chr6:28831926..28832649,2	Hela-S3	cervix:
5	chr11:10324730..10325418-chr6:109702760..109703284,2	Hela-S3	cervix:
6	chr11:9777333..9782154-chr11:10324598..10331360,10	MCF-7	breast:
7	chr11:10293712..10297432-chr11:10324720..10326890,3	MCF-7	breast:
8	chr11:10324505..10325396-chr5:139780169..139781064,2	Hela-S3	cervix:
9	chr11:10325263..10325959-chr19:13056797..13057297,2	Hela-S3	cervix:
10	chr11:10325124..10325825-chr16:3029973..3030914,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SBF2-1	chr11:10323789-10326390	NONHSAT017959

Variant related genes	Relation type
AMPD3	TF binding region
ADM	TF binding region
ENSG00000254554	TF binding region
ENSG00000245522	Chromatin interaction
ENSG00000133805	Chromatin interaction
ENSG00000127564	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000133812	Chromatin interaction
ENSG00000246273	Chromatin interaction
ENSG00000072952	Chromatin interaction
ENSG00000254719	Chromatin interaction
ENSG00000179262	Chromatin interaction
ENSG00000249637	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10160247	0.82[ASN][1000 genomes]
rs10160669	0.82[ASN][1000 genomes]
rs10160692	0.82[ASN][1000 genomes]
rs10500718	0.82[ASN][1000 genomes]
rs10500719	0.82[ASN][1000 genomes]
rs10500720	0.83[ASN][1000 genomes]
rs10500723	0.83[ASN][1000 genomes]
rs10743132	0.89[ASN][1000 genomes]
rs10840379	0.89[ASN][1000 genomes]
rs10840384	0.89[ASN][1000 genomes]
rs10840386	0.81[ASN][1000 genomes]
rs11042650	0.82[ASN][1000 genomes]
rs11042652	0.84[ASN][1000 genomes]
rs11042653	0.84[ASN][1000 genomes]
rs11042656	0.85[ASN][1000 genomes]
rs11042657	0.85[ASN][1000 genomes]
rs11042659	0.85[ASN][1000 genomes]
rs11042661	0.85[ASN][1000 genomes]
rs11042663	0.85[ASN][1000 genomes]
rs11042664	0.85[ASN][1000 genomes]
rs11042666	0.86[ASN][1000 genomes]
rs11042686	0.88[ASN][1000 genomes]
rs11042689	0.89[ASN][1000 genomes]
rs11042717	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11607621	0.89[ASN][1000 genomes]
rs12274104	0.84[ASN][1000 genomes]
rs12275224	0.85[ASN][1000 genomes]
rs12277662	0.82[ASN][1000 genomes]
rs12278680	0.87[ASN][1000 genomes]
rs12278735	0.84[ASN][1000 genomes]
rs12280005	0.86[ASN][1000 genomes]
rs12281409	0.87[ASN][1000 genomes]
rs12281526	0.85[ASN][1000 genomes]
rs12282974	0.87[ASN][1000 genomes]
rs12284884	0.85[ASN][1000 genomes]
rs12286545	0.87[ASN][1000 genomes]
rs12286927	0.84[ASN][1000 genomes]
rs12287386	0.84[ASN][1000 genomes]
rs12288200	0.85[ASN][1000 genomes]
rs12288275	0.85[ASN][1000 genomes]
rs12288486	0.84[ASN][1000 genomes]
rs12288654	0.85[ASN][1000 genomes]
rs12291196	0.84[ASN][1000 genomes]
rs12291198	0.84[ASN][1000 genomes]
rs12291253	0.82[ASN][1000 genomes]
rs12293757	0.82[ASN][1000 genomes]
rs12418494	0.81[ASN][1000 genomes]
rs12418690	0.89[ASN][1000 genomes]
rs12419064	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13377397	0.82[ASN][1000 genomes]
rs1442733	0.85[ASN][1000 genomes]
rs1442734	0.85[ASN][1000 genomes]
rs1442735	0.81[ASN][1000 genomes]
rs1442736	0.85[ASN][1000 genomes]
rs16907515	0.82[ASN][1000 genomes]
rs16907519	0.82[ASN][1000 genomes]
rs16907527	0.82[ASN][1000 genomes]
rs16907528	0.82[ASN][1000 genomes]
rs16907533	0.82[ASN][1000 genomes]
rs16907544	0.84[ASN][1000 genomes]
rs16907552	0.84[ASN][1000 genomes]
rs16907554	0.84[ASN][1000 genomes]
rs16907561	0.85[ASN][1000 genomes]
rs16907564	0.85[ASN][1000 genomes]
rs16907568	0.85[ASN][1000 genomes]
rs16907575	0.87[ASN][1000 genomes]
rs16907615	0.89[ASN][1000 genomes]
rs16907635	0.87[ASN][1000 genomes]
rs1822294	0.87[ASN][1000 genomes]
rs1822295	0.87[ASN][1000 genomes]
rs1867136	0.86[ASN][1000 genomes]
rs1867137	0.86[ASN][1000 genomes]
rs1867138	0.86[ASN][1000 genomes]
rs2028575	0.82[ASN][1000 genomes]
rs2028576	0.82[ASN][1000 genomes]
rs2028577	0.82[ASN][1000 genomes]
rs2028578	0.82[ASN][1000 genomes]
rs2069214	0.85[ASN][1000 genomes]
rs2119991	0.86[ASN][1000 genomes]
rs2278628	0.82[ASN][1000 genomes]
rs2278630	0.82[ASN][1000 genomes]
rs2278632	0.82[ASN][1000 genomes]
rs2278633	0.82[ASN][1000 genomes]
rs2920147	0.82[ASN][1000 genomes]
rs2957671	0.89[ASN][1000 genomes]
rs2957674	0.89[ASN][1000 genomes]
rs2957699	0.89[ASN][1000 genomes]
rs35598338	0.89[ASN][1000 genomes]
rs3814700	0.96[ASN][1000 genomes]
rs4076050	0.88[ASN][1000 genomes]
rs4399321	0.97[ASN][1000 genomes]
rs4418806	0.83[ASN][1000 genomes]
rs4444073	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4543988	0.82[ASN][1000 genomes]
rs4622247	0.82[ASN][1000 genomes]
rs4641466	0.97[ASN][1000 genomes]
rs56776911	0.83[ASN][1000 genomes]
rs57153895	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57521137	0.84[ASN][1000 genomes]
rs57522724	0.84[ASN][1000 genomes]
rs57595438	0.85[ASN][1000 genomes]
rs58340019	0.87[ASN][1000 genomes]
rs59717668	0.93[ASN][1000 genomes]
rs60319025	0.85[ASN][1000 genomes]
rs60578195	0.82[ASN][1000 genomes]
rs61149838	0.82[ASN][1000 genomes]
rs61889798	0.89[ASN][1000 genomes]
rs7107727	0.94[ASN][1000 genomes]
rs7115142	0.81[ASN][1000 genomes]
rs7924631	0.84[ASN][1000 genomes]
rs7927874	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933018	0.89[ASN][1000 genomes]
rs7935242	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952229	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11042725	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10323200-10329800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr11:10323200-10330200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr11:10323400-10325400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:10323400-10325800	Flanking Active TSS	HMEC	breast
5	chr11:10323600-10325400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:10323600-10325600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr11:10323600-10330000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr11:10323800-10326200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr11:10323800-10326600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:10323800-10326800	Active TSS	Brain Angular Gyrus	brain
11	chr11:10323800-10326800	Active TSS	NHLF	lung
12	chr11:10323800-10327200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:10323800-10327400	Active TSS	Rectal Smooth Muscle	rectum
14	chr11:10323800-10329000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr11:10323800-10329600	Active TSS	Placenta Amnion	Placenta Amnion
16	chr11:10323800-10330000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr11:10323800-10330000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr11:10323800-10330200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr11:10324000-10325400	Active TSS	Colonic Mucosa	Colon
20	chr11:10324000-10325600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
21	chr11:10324000-10326400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:10324000-10326600	Active TSS	Fetal Intestine Small	intestine
23	chr11:10324000-10327200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:10324000-10327200	Active TSS	A549	lung
25	chr11:10324000-10328200	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr11:10324000-10328600	Flanking Bivalent TSS/Enh	Dnd41	blood
27	chr11:10324000-10329200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr11:10324000-10329800	Active TSS	Aorta	Aorta
29	chr11:10324000-10330000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
30	chr11:10324000-10330000	Active TSS	Psoas Muscle	Psoas
31	chr11:10324000-10330200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr11:10324200-10325400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr11:10324200-10325400	Active TSS	Left Ventricle	heart
34	chr11:10324200-10325600	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr11:10324200-10325600	Active TSS	Hela-S3	cervix
36	chr11:10324200-10325600	Active TSS	Monocytes-CD14+_RO01746	blood
37	chr11:10324200-10325600	Active TSS	NHDF-Ad	bronchial
38	chr11:10324200-10325600	Active TSS	NHEK	skin
39	chr11:10324200-10326000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
40	chr11:10324200-10326200	Bivalent/Poised TSS	HepG2	liver
41	chr11:10324200-10326800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:10324200-10327400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:10324200-10327400	Active TSS	Fetal Kidney	kidney
44	chr11:10324200-10328000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:10324200-10328000	Active TSS	Small Intestine	intestine
46	chr11:10324200-10329800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr11:10324200-10329800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:10324200-10329800	Active TSS	Gastric	stomach
49	chr11:10324400-10327600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr11:10324400-10329800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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