Variant report

Variant	rs2232912
Chromosome Location	chr11:10879926-10879927
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	STAT1	chr11:10879134-10880575	GM12878	blood:	n/a	chr11:10879458-10879470 chr11:10879347-10879356 chr11:10879348-10879357 chr11:10879346-10879357 chr11:10879466-10879478
2	MXI1	chr11:10878921-10879957	K562	blood:	n/a	n/a
3	RELA	chr11:10878559-10880078	GM18951	blood:	n/a	n/a
4	GATA2	chr11:10878725-10880523	SH-SY5Y	brain:	n/a	chr11:10879725-10879735 chr11:10878920-10878928
5	RAD21	chr11:10879158-10880584	IMR90	lung:	n/a	chr11:10879757-10879771
6	TBL1XR1	chr11:10878820-10880067	GM12878	blood:	n/a	n/a
7	BRCA1	chr11:10879372-10879956	GM12878	blood:	n/a	n/a
8	GTF2B	chr11:10879354-10880094	K562	blood:	n/a	n/a
9	POLR2A	chr11:10878541-10880785	H1-neurons	neurons:	n/a	n/a
10	MXI1	chr11:10878770-10880654	Hela-S3	cervix:	n/a	n/a
11	CHD2	chr11:10878928-10880663	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:10878385-10880725	GM19099	blood:	n/a	n/a
13	MAX	chr11:10879695-10880550	K562	blood:	n/a	n/a
14	POLR2A	chr11:10878578-10880672	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:10878698-10880655	NB4	blood:	n/a	n/a
16	WRNIP1	chr11:10878375-10880154	GM12878	blood:	n/a	n/a
17	GATA1	chr11:10878731-10880676	PBDE	blood:	n/a	chr11:10879725-10879735 chr11:10878920-10878928
18	POLR2A	chr11:10878661-10880620	HCT-116	colon:	n/a	n/a
19	POLR2A	chr11:10878442-10880641	HL-60	blood:	n/a	n/a
20	POLR2A	chr11:10878833-10879977	HepG2	liver:	n/a	n/a
21	FOS	chr11:10879650-10880141	MCF10A-Er-Src	breast:	n/a	chr11:10879712-10879721
22	SIN3AK20	chr11:10879717-10880004	SK-N-SH	brain:	n/a	n/a
23	TAF1	chr11:10879143-10879944	GM12892	blood:	n/a	n/a
24	RFX5	chr11:10879491-10879964	H1-hESC	embryonic stem cell:	n/a	n/a
25	ARID3A	chr11:10879350-10880200	K562	blood:	n/a	n/a
26	POLR2A	chr11:10878798-10880543	H1-hESC	embryonic stem cell:	n/a	n/a
27	IRF3	chr11:10879372-10879926	Hela-S3	cervix:	n/a	chr11:10879483-10879495 chr11:10879476-10879496 chr11:10879712-10879726
28	YY1	chr11:10878905-10880001	NT2-D1	testis:	n/a	chr11:10879332-10879340 chr11:10879385-10879394 chr11:10879331-10879353 chr11:10879331-10879341 chr11:10879457-10879468 chr11:10879285-10879296 chr11:10879578-10879589
29	TAL1	chr11:10878891-10880395	K562	blood:	n/a	chr11:10879003-10879018 chr11:10879003-10879018
30	HCFC1	chr11:10878896-10880517	K562	blood:	n/a	n/a
31	RELA	chr11:10878283-10880584	GM15510	blood:	n/a	n/a
32	PAX5	chr11:10879066-10880107	GM12878	blood:	n/a	chr11:10879707-10879724 chr11:10879705-10879723 chr11:10879706-10879725
33	POLR2A	chr11:10878583-10880601	GM12892	blood:	n/a	n/a
34	ATF3	chr11:10879267-10880604	A549	lung:	n/a	chr11:10880448-10880456
35	NANOG	chr11:10879175-10880053	H1-hESC	embryonic stem cell:	n/a	chr11:10879481-10879495
36	ELK1	chr11:10878537-10879987	GM12878	blood:	n/a	n/a
37	HDAC2	chr11:10879260-10879953	K562	blood:	n/a	n/a
38	EP300	chr11:10879234-10879949	SK-N-SH_RA	brain:	n/a	chr11:10879387-10879396 chr11:10879700-10879716 chr11:10879485-10879499
39	TFAP2C	chr11:10878652-10880638	Hela-S3	cervix:	n/a	chr11:10880427-10880442
40	TAF1	chr11:10879129-10879978	GM12891	blood:	n/a	n/a
41	USF2	chr11:10879341-10880069	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr11:10878859-10880496	A549	lung:	n/a	n/a
43	STAT3	chr11:10879316-10880197	Hela-S3	cervix:	n/a	chr11:10879346-10879357 chr11:10879458-10879470 chr11:10879347-10879356 chr11:10879348-10879357 chr11:10879466-10879478
44	POLR2A	chr11:10878831-10879991	H1-hESC	embryonic stem cell:	n/a	n/a
45	TBP	chr11:10878399-10880694	K562	blood:	n/a	n/a
46	RELA	chr11:10878446-10880134	GM18505	blood:	n/a	n/a
47	FOS	chr11:10879524-10880096	Hela-S3	cervix:	n/a	chr11:10879712-10879721
48	POLR2A	chr11:10878576-10880082	GM12891	blood:	n/a	n/a
49	SIN3AK20	chr11:10879104-10880622	PANC-1	pancreas:	n/a	n/a
50	TCF12	chr11:10879205-10879957	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10879199..10879959-chr5:172198027..172198617,2	Hela-S3	cervix:
2	chr11:10879316..10880187-chr6:125622429..125623389,2	HCT-116	colon:
3	chr11:10877728..10881491-chr11:10917238..10922801,13	MCF-7	breast:
4	chr11:10878223..10880538-chr11:10918318..10920924,5	K562	blood:
5	chr11:10830617..10831380-chr11:10879218..10880193,3	MCF-7	breast:
6	chr11:10875813..10884237-chr11:10918851..10925690,14	K562	blood:
7	chr11:10826628..10833192-chr11:10862494..10882277,65	MCF-7	breast:
8	chr11:10879660..10880286-chr3:119813936..119814914,2	Hela-S3	cervix:
9	chr11:10827202..10834699-chr11:10873450..10884211,37	MCF-7	breast:
10	chr11:10821010..10837911-chr11:10870747..10882644,62	K562	blood:
11	chr11:10821312..10832598-chr11:10875146..10882197,42	K562	blood:
12	chr11:10879693..10880601-chr12:64615799..64616338,2	Hela-S3	cervix:
13	chr11:10878419..10881126-chr11:11862004..11864876,2	K562	blood:
14	chr11:10822401..10824096-chr11:10878190..10881156,2	MCF-7	breast:
15	chr11:10879491..10880058-chr19:751095..751744,2	Hela-S3	cervix:
16	chr11:10822404..10825396-chr11:10877343..10880105,2	MCF-7	breast:
17	chr11:10879256..10880017-chr17:7387378..7388075,3	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTR9-3	chr11:10879815-10880489	ENSG00000247271

Variant related genes	Relation type
ZBED5	TF binding region
ENSG00000120129	Chromatin interaction
ENSG00000243024	Chromatin interaction
ENSG00000111906	Chromatin interaction
ENSG00000099812	Chromatin interaction
ENSG00000246308	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000250041	Chromatin interaction
ENSG00000242622	Chromatin interaction
ENSG00000170242	Chromatin interaction
ENSG00000174206	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000238622	Chromatin interaction
ENSG00000181222	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11042942	1.00[EUR][1000 genomes]
rs11821886	1.00[AMR][1000 genomes]
rs11822861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11823290	1.00[ASW][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11827592	1.00[AMR][1000 genomes]
rs55730838	1.00[AMR][1000 genomes]
rs56009251	1.00[AMR][1000 genomes]
rs56161511	1.00[AMR][1000 genomes]
rs57991096	1.00[AMR][1000 genomes]
rs58366863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58432384	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58560142	1.00[AMR][1000 genomes]
rs59239356	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59433293	1.00[AMR][1000 genomes]
rs59882147	1.00[EUR][1000 genomes]
rs60370256	1.00[EUR][1000 genomes]
rs61997166	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419666	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419672	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73419674	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419678	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419688	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419698	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419699	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73419702	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73421505	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73421506	1.00[EUR][1000 genomes]
rs73421514	1.00[EUR][1000 genomes]
rs73421517	1.00[EUR][1000 genomes]
rs73421520	1.00[EUR][1000 genomes]
rs73421534	1.00[EUR][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	nsv1040606	chr11:10763753-10995698	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2232912	CD4	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10876800-10880800	Active TSS	Fetal Brain Female	brain
2	chr11:10877200-10881200	Active TSS	GM12878-XiMat	blood
3	chr11:10877600-10880400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr11:10877600-10881000	Active TSS	Fetal Muscle Leg	muscle
5	chr11:10877600-10881200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:10877600-10881200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:10877600-10881200	Active TSS	Psoas Muscle	Psoas
8	chr11:10877600-10881200	Active TSS	NHLF	lung
9	chr11:10877800-10880200	Active TSS	HMEC	breast
10	chr11:10877800-10881000	Active TSS	HSMMtube	muscle
11	chr11:10877800-10881200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr11:10877800-10881200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr11:10877800-10881400	Active TSS	Stomach Smooth Muscle	stomach
14	chr11:10877800-10881400	Active TSS	K562	blood
15	chr11:10877800-10881600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:10878000-10880800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:10878000-10880800	Active TSS	Right Ventricle	heart
18	chr11:10878000-10881000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr11:10878000-10881000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:10878000-10881000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:10878000-10881000	Active TSS	Fetal Stomach	stomach
22	chr11:10878000-10881000	Active TSS	Fetal Thymus	thymus
23	chr11:10878000-10881000	Active TSS	HSMM	muscle
24	chr11:10878000-10881200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:10878000-10881200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr11:10878000-10881200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:10878000-10881200	Active TSS	Aorta	Aorta
28	chr11:10878000-10881400	Active TSS	NHDF-Ad	bronchial
29	chr11:10878000-10881600	Active TSS	Muscle Satellite Cultured Cells	--
30	chr11:10878000-10881600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:10878200-10880400	Active TSS	Placenta	Placenta
32	chr11:10878200-10880600	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr11:10878200-10880600	Active TSS	Rectal Smooth Muscle	rectum
34	chr11:10878200-10880800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:10878200-10880800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:10878200-10880800	Active TSS	Colonic Mucosa	Colon
37	chr11:10878200-10880800	Active TSS	Fetal Muscle Trunk	muscle
38	chr11:10878200-10880800	Active TSS	Left Ventricle	heart
39	chr11:10878200-10880800	Active TSS	Ovary	ovary
40	chr11:10878200-10880800	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr11:10878200-10881000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:10878200-10881000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:10878200-10881000	Active TSS	Colon Smooth Muscle	Colon
44	chr11:10878200-10881000	Active TSS	Fetal Intestine Large	intestine
45	chr11:10878200-10881000	Active TSS	Fetal Intestine Small	intestine
46	chr11:10878200-10881000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr11:10878200-10881200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:10878200-10881400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:10878200-10881400	Active TSS	Fetal Lung	lung
50	chr11:10878400-10880600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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