Variant report

Variant	rs4987878
Chromosome Location	chr11:108093002-108093003
allele	G/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	POLR2A	chr11:108092725-108094760	K562	blood:	n/a	n/a
2	HCFC1	chr11:108092888-108095065	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:108091677-108096659	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:108092409-108094595	HEK293	kidney:	n/a	n/a
5	RELA	chr11:108092503-108094123	GM19193	blood:	n/a	n/a
6	POLR2A	chr11:108092979-108094242	MCF-7	breast:	n/a	n/a
7	RELA	chr11:108092623-108095186	GM19099	blood:	n/a	n/a
8	MAX	chr11:108092968-108094500	SK-N-SH	brain:	n/a	chr11:108093678-108093685
9	ZEB1	chr11:108092649-108093057	GM12878	blood:	n/a	n/a
10	MAX	chr11:108092922-108094328	A549	lung:	n/a	chr11:108093678-108093685
11	POLR2A	chr11:108092834-108094975	IMR90	lung:	n/a	n/a
12	E2F6	chr11:108092997-108093949	K562	blood:	n/a	chr11:108093428-108093445 chr11:108093619-108093628 chr11:108093431-108093438 chr11:108093515-108093527 chr11:108093431-108093442 chr11:108093405-108093414
13	SIN3AK20	chr11:108092928-108094416	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr11:108092617-108094171	GM12878	blood:	n/a	n/a
15	YY1	chr11:108092620-108094212	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:108092729-108094408	SK-N-MC	brain:	n/a	n/a
17	CREB1	chr11:108092924-108094814	K562	blood:	n/a	n/a
18	POLR2A	chr11:108092551-108094701	K562	blood:	n/a	n/a
19	POLR2A	chr11:108091635-108094953	PBDE	blood:	n/a	n/a
20	TAF1	chr11:108092692-108094316	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr11:108092916-108094668	K562	blood:	n/a	n/a
22	MAZ	chr11:108092096-108094312	IMR90	lung:	n/a	chr11:108093678-108093685
23	POLR2A	chr11:108092751-108094204	K562	blood:	n/a	n/a
24	RELA	chr11:108092324-108095081	GM15510	blood:	n/a	n/a
25	MXI1	chr11:108092715-108094317	Hela-S3	cervix:	n/a	n/a
26	TAF1	chr11:108092940-108094297	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr11:108092929-108094222	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr11:108092978-108094561	PANC-1	pancreas:	n/a	n/a
29	CREB1	chr11:108092994-108094156	HepG2	liver:	n/a	n/a
30	GABPA	chr11:108092993-108093949	A549	lung:	n/a	chr11:108093618-108093629 chr11:108093615-108093629 chr11:108093694-108093705
31	SPI1	chr11:108092866-108094207	HL-60	blood:	n/a	chr11:108094030-108094043 chr11:108093745-108093758
32	POLR2A	chr11:108092570-108094851	HepG2	liver:	n/a	n/a
33	TBP	chr11:108092970-108094145	HepG2	liver:	n/a	n/a
34	MTA3	chr11:108092748-108093464	GM12878	blood:	n/a	n/a
35	TCF7L2	chr11:108092600-108094421	PANC-1	pancreas:	n/a	chr11:108092640-108092649 chr11:108092636-108092652 chr11:108094194-108094208 chr11:108094193-108094209 chr11:108094193-108094209 chr11:108092636-108092652
36	POLR2A	chr11:108092734-108094923	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:108092881-108094970	NB4	blood:	n/a	n/a
38	E2F1	chr11:108092696-108094042	Hela-S3	cervix:	n/a	chr11:108093428-108093445 chr11:108093619-108093628 chr11:108093431-108093438 chr11:108093515-108093527 chr11:108093431-108093442 chr11:108093405-108093414
39	NRF1	chr11:108092650-108094424	SK-N-SH	brain:	n/a	chr11:108093618-108093629 chr11:108093615-108093629 chr11:108093693-108093704 chr11:108093694-108093705
40	POLR2A	chr11:108092947-108094286	HepG2	liver:	n/a	n/a
41	UBTF	chr11:108092513-108094675	K562	blood:	n/a	n/a
42	GTF2F1	chr11:108092716-108094336	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr11:108092516-108095295	GM19099	blood:	n/a	n/a
44	MAX	chr11:108092942-108094099	MCF-7	breast:	n/a	chr11:108093678-108093685
45	TAF7	chr11:108092876-108093514	H1-hESC	embryonic stem cell:	n/a	n/a
46	STAT1	chr11:108092691-108094107	GM12878	blood:	n/a	chr11:108093502-108093514
47	MAX	chr11:108092592-108094081	ECC-1	luminal epithelium:	n/a	chr11:108093678-108093685
48	POLR2A	chr11:108092997-108094676	PANC-1	pancreas:	n/a	n/a
49	MAX	chr11:108092986-108094640	K562	blood:	n/a	chr11:108093678-108093685
50	TBL1XR1	chr11:108092516-108094196	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:108092964-108093014	A549	lung:	n/a
2	chr11:108092970-108093020	AG04449	skin:	fetal
3	chr11:108092964-108093014	AoSMC	blood vessel:	n/a
4	chr11:108092964-108093014	GM19239	blood:	n/a
5	chr11:108092964-108093014	AG09319	gingival:	n/a
6	chr11:108092964-108093014	ProgFib	skin:	n/a
7	chr11:108092970-108093020	HepG2	liver:	n/a
8	chr11:108092970-108093020	Hepatocyte	liver:	n/a
9	chr11:108092970-108093020	T-47D	breast:	n/a
10	chr11:108092970-108093020	LNCaP	prostate:	n/a
11	chr11:108092964-108093014	Hela-S3	cervix:	n/a
12	chr11:108092964-108093014	AG04450	lung:	fetal
13	chr11:108092970-108093020	ovcar-3	ovarian:	n/a
14	chr11:108092964-108093014	K562	blood:	n/a
15	chr11:108092970-108093020	HRCEpiC	kidney:	n/a
16	chr11:108092964-108093014	U87	brain:	n/a
17	chr11:108092964-108093014	AG09309	skin:	n/a
18	chr11:108092970-108093020	Hela-S3	cervix:	n/a
19	chr11:108092964-108093014	Hepatocyte	liver:	n/a
20	chr11:108092964-108093014	T-47D	breast:	n/a
21	chr11:108092970-108093020	ECC-1	luminal epithelium:	n/a
22	chr11:108092964-108093014	GM06990	blood:	n/a
23	chr11:108092964-108093014	SK-N-MC	brain:	n/a
24	chr11:108092970-108093020	NHBE	bronchial:	n/a
25	chr11:108092964-108093014	HCPEpiC	choroid plexus:	n/a
26	chr11:108092964-108093014	SAEC	small airway:	n/a
27	chr11:108092964-108093014	SK-N-SH_RA	brain:	n/a
28	chr11:108092970-108093020	SK-N-SH_RA	brain:	n/a
29	chr11:108092970-108093020	SK-N-MC	brain:	n/a
30	chr11:108092964-108093014	HMEC	breast:	n/a
31	chr11:108092964-108093014	CMK	blood:	n/a
32	chr11:108092970-108093020	GM06990	blood:	n/a
33	chr11:108092964-108093014	BJ	skin:	n/a
34	chr11:108092970-108093020	HEEpiC	esophagus:	n/a
35	chr11:108092970-108093020	NT2-D1	testis:	n/a
36	chr11:108092964-108093014	HEEpiC	esophagus:	n/a
37	chr11:108092964-108093014	PFSK-1	brain:	n/a
38	chr11:108092970-108093020	Caco-2	colon:	n/a
39	chr11:108092964-108093014	HepG2	liver:	n/a
40	chr11:108092964-108093014	GM12892	blood:	n/a
41	chr11:108092970-108093020	AG04450	lung:	fetal
42	chr11:108092970-108093020	AoSMC	blood vessel:	n/a
43	chr11:108092964-108093014	ECC-1	luminal epithelium:	n/a
44	chr11:108092964-108093014	HNPCEpiC	eye:	n/a
45	chr11:108092970-108093020	CMK	blood:	n/a
46	chr11:108092964-108093014	LNCaP	prostate:	n/a
47	chr11:108092964-108093014	HEK293	kidney:	embryo
48	chr11:108092970-108093020	SK-N-SH	brain:	n/a
49	chr11:108092964-108093014	HUVEC	blood vessel:	n/a
50	chr11:108092970-108093020	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:108092929..108093774-chr17:7475339..7476197,2	Hela-S3	cervix:
2	chr11:108092115..108094604-chr11:108367755..108370100,3	K562	blood:
3	chr11:108091790..108094967-chr11:108462852..108466169,3	K562	blood:
4	chr11:108092760..108095657-chr11:108096566..108100675,5	MCF-7	breast:
5	chr11:108092435..108094238-chr11:110158688..110160206,2	MCF-7	breast:
6	chr11:107992282..107994125-chr11:108092449..108094486,3	K562	blood:
7	chr11:108092141..108094808-chr11:108335621..108340680,5	K562	blood:
8	chr11:108092327..108094549-chr11:108338651..108340680,2	K562	blood:
9	chr11:108092600..108095376-chr11:108462934..108465266,2	MCF-7	breast:
10	chr11:108092910..108093711-chr15:65282014..65282828,2	Hela-S3	cervix:

Variant related genes	Relation type
ATM	TF binding region
ATM	CpG island
ENSG00000178202	Chromatin interaction
ENSG00000161960	Chromatin interaction
ENSG00000137710	Chromatin interaction
ENSG00000255467	Chromatin interaction
ENSG00000110723	Chromatin interaction
ENSG00000206967	Chromatin interaction
ENSG00000166323	Chromatin interaction
ENSG00000090487	Chromatin interaction
ENSG00000221607	Chromatin interaction
ENSG00000075239	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11821299	1.00[YRI][hapmap]
rs11825355	1.00[YRI][hapmap]
rs17107969	1.00[YRI][hapmap]
rs17107980	1.00[YRI][hapmap]
rs2234994	0.83[AFR][1000 genomes]
rs2235000	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2235001	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs3092836	1.00[YRI][hapmap]
rs3092856	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4987926	1.00[YRI][hapmap]
rs4987929	1.00[YRI][hapmap]
rs4988050	1.00[YRI][hapmap]
rs4988086	0.89[AFR][1000 genomes]
rs7119429	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7931985	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv898383	chr11:108068954-108251211	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4987878	C11orf65	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108090200-108095000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr11:108090800-108094800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:108091000-108094000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:108091000-108097400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:108091200-108093200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:108091200-108096200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:108091400-108093200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr11:108091400-108094400	Active TSS	K562	blood
9	chr11:108091600-108093200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr11:108091600-108093200	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr11:108091600-108093200	Active TSS	Right Atrium	heart
12	chr11:108091600-108093400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:108091600-108094400	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr11:108091600-108094400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr11:108091600-108094400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr11:108091600-108094600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr11:108091600-108094800	Active TSS	Hela-S3	cervix
18	chr11:108091600-108094800	Active TSS	NHDF-Ad	bronchial
19	chr11:108091600-108095400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:108091600-108095600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:108091800-108093200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr11:108091800-108093200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr11:108091800-108094200	Active TSS	Placenta	Placenta
24	chr11:108091800-108094400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:108091800-108094400	Active TSS	Fetal Intestine Large	intestine
26	chr11:108091800-108094400	Active TSS	Fetal Kidney	kidney
27	chr11:108091800-108094400	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr11:108091800-108094400	Active TSS	NHLF	lung
29	chr11:108091800-108094600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:108091800-108094600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:108091800-108094600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr11:108091800-108094600	Active TSS	HSMMtube	muscle
33	chr11:108091800-108094800	Active TSS	Lung	lung
34	chr11:108091800-108095000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:108091800-108095000	Active TSS	Colonic Mucosa	Colon
36	chr11:108091800-108095000	Active TSS	Left Ventricle	heart
37	chr11:108091800-108095000	Active TSS	GM12878-XiMat	blood
38	chr11:108091800-108095200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:108091800-108095400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr11:108091800-108096200	Active TSS	Primary T cells fromperipheralblood	blood
41	chr11:108091800-108096200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:108091800-108097000	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr11:108091800-108097000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr11:108091800-108098200	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr11:108092000-108094400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:108092000-108094400	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr11:108092000-108094400	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr11:108092000-108094400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:108092000-108094400	Active TSS	HSMM	muscle
50	chr11:108092000-108094400	Active TSS	NHEK	skin

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