Variant report

Variant	rs16938581
Chromosome Location	chr11:47271039-47271040
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	POLR2A	chr11:47269583-47271233	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOXA1	chr11:47270566-47271073	HepG2	liver:	n/a	n/a
3	TFAP2C	chr11:47270056-47271250	Hela-S3	cervix:	n/a	chr11:47270428-47270437
4	YY1	chr11:47269842-47271339	SK-N-SH	brain:	n/a	chr11:47270443-47270453 chr11:47270444-47270452 chr11:47270443-47270465
5	RFX5	chr11:47270198-47271092	HepG2	liver:	n/a	n/a
6	FOXA2	chr11:47270601-47271155	A549	lung:	n/a	n/a
7	POLR2A	chr11:47269943-47271119	U87	brain:	n/a	n/a
8	POLR2A	chr11:47269971-47271213	HepG2	liver:	n/a	n/a
9	YY1	chr11:47269914-47271109	A549	lung:	n/a	chr11:47270443-47270453 chr11:47270444-47270452 chr11:47270443-47270465
10	GABPA	chr11:47269700-47271286	MCF-7	breast:	n/a	n/a
11	MBD4	chr11:47269988-47271180	HepG2	liver:	n/a	n/a
12	YY1	chr11:47269886-47271088	GM12878	blood:	n/a	chr11:47270443-47270453 chr11:47270444-47270452 chr11:47270443-47270465
13	MTA3	chr11:47269615-47271184	GM12878	blood:	n/a	n/a
14	FOXA2	chr11:47270601-47271040	HepG2	liver:	n/a	n/a
15	WRNIP1	chr11:47269632-47271071	GM12878	blood:	n/a	n/a
16	SIN3A	chr11:47269936-47271176	H1-hESC	embryonic stem cell:	n/a	n/a
17	HNF4A	chr11:47270246-47271292	HepG2	liver:	n/a	chr11:47270864-47270872 chr11:47270706-47270713
18	FOXA2	chr11:47270361-47271437	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:47269600-47271223	PFSK-1	brain:	n/a	n/a
20	EP300	chr11:47270135-47271072	HepG2	liver:	n/a	chr11:47270429-47270436 chr11:47270940-47270954
21	MYBL2	chr11:47270041-47271236	HepG2	liver:	n/a	n/a
22	POLR2A	chr11:47270113-47271188	HepG2	liver:	n/a	n/a
23	GABPA	chr11:47269946-47271117	SK-N-SH	brain:	n/a	n/a
24	CHD1	chr11:47269694-47271051	IMR90	lung:	n/a	n/a
25	JUN	chr11:47269740-47271436	K562	blood:	n/a	n/a
26	HEY1	chr11:47270172-47271323	HepG2	liver:	n/a	n/a
27	NFIC	chr11:47270159-47271060	HepG2	liver:	n/a	n/a
28	YY1	chr11:47270140-47271094	GM12891	blood:	n/a	chr11:47270443-47270453 chr11:47270444-47270452 chr11:47270443-47270465
29	POLR2A	chr11:47269643-47271255	HepG2	liver:	n/a	n/a
30	HCFC1	chr11:47268991-47271448	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr11:47269723-47271156	K562	blood:	n/a	n/a
32	SIX5	chr11:47269676-47271084	A549	lung:	n/a	n/a
33	HNF4G	chr11:47270655-47271056	HepG2	liver:	n/a	chr11:47270864-47270872 chr11:47270859-47270874 chr11:47270706-47270713
34	POLR2A	chr11:47269951-47271070	H1-neurons	neurons:	n/a	n/a
35	FOXA1	chr11:47270138-47271069	HepG2	liver:	n/a	n/a
36	REST	chr11:47269562-47271201	H1-neurons	neurons:	n/a	chr11:47270965-47270978
37	MXI1	chr11:47269274-47271302	SK-N-SH	brain:	n/a	n/a
38	GABPA	chr11:47269764-47271178	A549	lung:	n/a	n/a
39	EP300	chr11:47269968-47271163	A549	lung:	n/a	chr11:47270429-47270436 chr11:47270940-47270954
40	SIN3AK20	chr11:47269837-47271188	MCF-7	breast:	n/a	n/a
41	POLR2A	chr11:47269927-47271419	SK-N-MC	brain:	n/a	n/a
42	MAX	chr11:47270061-47271068	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr11:47269949-47271067	U87	brain:	n/a	n/a
44	SMC3	chr11:47270276-47271159	HepG2	liver:	n/a	n/a
45	STAT5A	chr11:47269704-47271042	GM12878	blood:	n/a	chr11:47270944-47270955 chr11:47269770-47269777
46	BCL3	chr11:47270119-47271082	A549	lung:	n/a	chr11:47270428-47270437 chr11:47270940-47270949
47	NR2F2	chr11:47269544-47271208	K562	blood:	n/a	n/a
48	FOXA1	chr11:47270235-47271107	HepG2	liver:	n/a	n/a
49	SIN3A	chr11:47269954-47271043	GM12878	blood:	n/a	n/a
50	FOXA1	chr11:47270174-47271058	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47270160..47271139-chr17:47491742..47492390,2	NB4	blood:
2	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
3	chr11:47234882..47238296-chr11:47268822..47272499,5	MCF-7	breast:
4	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:
5	chr11:47268303..47273264-chr11:47289525..47294481,12	K562	blood:
6	chr11:47212303..47214125-chr11:47270585..47273410,2	MCF-7	breast:
7	chr11:47269451..47271860-chr11:47428590..47432270,5	K562	blood:
8	chr11:47263865..47272320-chr11:47288426..47294726,14	MCF-7	breast:
9	chr11:47270637..47271249-chr11:47291585..47292264,2	MCF-7	breast:
10	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
11	chr11:47270160..47271139-chr15:74753403..74754116,2	NB4	blood:
12	chr11:47267881..47272421-chr11:47288787..47294481,12	K562	blood:
13	chr11:47270532..47273351-chr11:47280081..47283365,3	K562	blood:
14	chr11:47197356..47201056-chr11:47268366..47272336,6	MCF-7	breast:
15	chr11:47263774..47268457-chr11:47268937..47272422,6	MCF-7	breast:
16	chr11:47205635..47209843-chr11:47268961..47271979,7	MCF-7	breast:
17	chr11:47268938..47272778-chr11:47288986..47293565,7	MCF-7	breast:
18	chr11:47270967..47273791-chr11:47284181..47286277,2	K562	blood:

Variant related genes	Relation type
ACP2	TF binding region
ENSG00000025434	Chromatin interaction
ENSG00000243802	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000255197	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000247240	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000138629	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000167085	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1051006	0.80[AMR][1000 genomes]
rs10838681	0.88[AFR][1000 genomes]
rs10838685	0.81[EUR][1000 genomes]
rs11039144	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11039148	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039155	0.86[EUR][1000 genomes]
rs12574081	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1449626	0.80[AMR][1000 genomes]
rs2242261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279238	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2306353	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2596397	0.89[AMR][1000 genomes]
rs2596398	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2633080	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2633083	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2957873	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs326224	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758670	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781619	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3781620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3824866	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647725	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4647726	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4647737	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647741	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647754	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647757	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4752972	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752973	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs4752977	0.81[AMR][1000 genomes]
rs59567949	0.80[AMR][1000 genomes]
rs7118396	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7395496	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7933246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947269	0.83[AMR][1000 genomes]
rs830083	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830084	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16938581	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs16938581	ACP2	cis	Thyroid	GTEx
rs16938581	ACP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47269000-47271400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr11:47269200-47271200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr11:47269200-47271400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr11:47269200-47271400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr11:47269400-47271400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr11:47269400-47271400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:47269400-47271400	Active TSS	A549	lung
8	chr11:47269400-47271600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:47269600-47271200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:47269600-47271400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:47269600-47271400	Active TSS	H9 Cell Line	embryonic stem cell
12	chr11:47269600-47272000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:47269800-47271200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:47269800-47271200	Active TSS	Ovary	ovary
15	chr11:47269800-47271200	Bivalent/Poised TSS	HepG2	liver
16	chr11:47269800-47271200	Active TSS	K562	blood
17	chr11:47269800-47271400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:47269800-47271400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:47269800-47271400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:47269800-47271400	Active TSS	Colonic Mucosa	Colon
21	chr11:47269800-47271400	Active TSS	Fetal Kidney	kidney
22	chr11:47270000-47271200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:47270000-47271200	Active TSS	Stomach Mucosa	stomach
24	chr11:47270000-47271400	Active TSS	Fetal Brain Female	brain
25	chr11:47270600-47271200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr11:47270600-47271200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:47270600-47271200	Flanking Active TSS	Pancreas	Pancrea
28	chr11:47270600-47271200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr11:47270600-47271200	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr11:47270600-47271400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr11:47270600-47271400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr11:47270600-47271400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:47270600-47271400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:47270600-47271400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:47270600-47271400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr11:47270600-47271400	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr11:47270800-47271200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:47270800-47271200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:47270800-47271200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:47270800-47271200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:47270800-47271200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr11:47270800-47271200	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr11:47270800-47271200	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr11:47270800-47271200	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr11:47270800-47271200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr11:47270800-47271200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr11:47270800-47271200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr11:47270800-47271200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr11:47270800-47271200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr11:47270800-47271200	Flanking Active TSS	Esophagus	oesophagus

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