Variant report

Variant	rs3758673
Chromosome Location	chr11:47278917-47278918
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	MBD4	chr11:47278889-47279372	HepG2	liver:	n/a	n/a
2	HNF4G	chr11:47278894-47279567	HepG2	liver:	n/a	chr11:47279169-47279181
3	MAZ	chr11:47278766-47279794	Hela-S3	cervix:	n/a	chr11:47279428-47279438
4	EP300	chr11:47278888-47279390	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:47278753-47279854	H1-hESC	embryonic stem cell:	n/a	n/a
6	TFAP2A	chr11:47278615-47279625	Hela-S3	cervix:	n/a	chr11:47279422-47279434 chr11:47279422-47279434 chr11:47279093-47279108 chr11:47278730-47278740 chr11:47279422-47279434 chr11:47278973-47278985 chr11:47278730-47278740 chr11:47278730-47278740 chr11:47279060-47279070 chr11:47278730-47278740 chr11:47278973-47278985 chr11:47278973-47278985 chr11:47279058-47279073 chr11:47279422-47279434
7	SIN3AK20	chr11:47278641-47279495	MCF-7	breast:	n/a	n/a
8	POLR2A	chr11:47278846-47279887	K562	blood:	n/a	n/a
9	MAX	chr11:47278830-47279539	HepG2	liver:	n/a	chr11:47279428-47279438
10	CEBPB	chr11:47278916-47279294	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr11:47278816-47279716	Hela-S3	cervix:	n/a	n/a
12	TCF7L2	chr11:47278821-47279270	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr11:47278556-47279740	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:47278849-47279347	SK-N-MC	brain:	n/a	n/a
15	MAX	chr11:47278875-47279698	A549	lung:	n/a	chr11:47279428-47279438
16	MAX	chr11:47278677-47279728	Hela-S3	cervix:	n/a	chr11:47279428-47279438
17	TAL1	chr11:47278817-47279092	K562	blood:	n/a	chr11:47278960-47278968
18	SMC3	chr11:47278690-47279821	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr11:47278875-47279947	HepG2	liver:	n/a	n/a
20	POLR2A	chr11:47278617-47279780	Hela-S3	cervix:	n/a	n/a
21	CEBPB	chr11:47278799-47279424	MCF-7	breast:	n/a	n/a
22	POLR2A	chr11:47278808-47279528	PFSK-1	brain:	n/a	n/a
23	HEY1	chr11:47278861-47279689	HepG2	liver:	n/a	n/a
24	MAX	chr11:47278853-47279583	A549	lung:	n/a	chr11:47279428-47279438
25	POLR2A	chr11:47278778-47279695	K562	blood:	n/a	n/a
26	POLR2A	chr11:47278872-47279742	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:47278878-47279674	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr11:47278739-47279809	Hela-S3	cervix:	n/a	n/a
29	SP1	chr11:47278875-47279483	A549	lung:	n/a	chr11:47279427-47279439 chr11:47279428-47279438 chr11:47279359-47279371 chr11:47279114-47279128 chr11:47279427-47279439 chr11:47279429-47279438 chr11:47279359-47279371 chr11:47279360-47279369 chr11:47279428-47279437 chr11:47279107-47279121 chr11:47279356-47279370
30	GTF2F1	chr11:47278683-47279672	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr11:47278850-47279806	PFSK-1	brain:	n/a	n/a
32	HNF4G	chr11:47278898-47279412	HepG2	liver:	n/a	chr11:47279169-47279181
33	POLR2A	chr11:47278832-47280214	K562	blood:	n/a	n/a
34	CTCF	chr11:47278588-47281976	A549	lung:	n/a	chr11:47278969-47278982
35	MAX	chr11:47278727-47279707	Hela-S3	cervix:	n/a	chr11:47279428-47279438
36	SMARCC1	chr11:47278643-47280119	Hela-S3	cervix:	n/a	n/a
37	BRCA1	chr11:47278904-47279651	Hela-S3	cervix:	n/a	n/a
38	SMARCB1	chr11:47278799-47280012	Hela-S3	cervix:	n/a	n/a
39	TBP	chr11:47278859-47279635	Hela-S3	cervix:	n/a	n/a
40	MAZ	chr11:47278807-47280171	IMR90	lung:	n/a	chr11:47279428-47279438
41	RFX5	chr11:47278730-47279777	Hela-S3	cervix:	n/a	n/a
42	RAD21	chr11:47278751-47279828	Hela-S3	cervix:	n/a	n/a
43	HCFC1	chr11:47278486-47281950	Hela-S3	cervix:	n/a	n/a
44	MXI1	chr11:47278814-47279598	Hela-S3	cervix:	n/a	n/a
45	TFAP2C	chr11:47278597-47279762	Hela-S3	cervix:	n/a	n/a
46	CEBPD	chr11:47278878-47279682	HepG2	liver:	n/a	n/a
47	TCF12	chr11:47278684-47279705	A549	lung:	n/a	n/a
48	CTCF	chr11:47278860-47279010	Hela-S3	cervix:	n/a	chr11:47278969-47278982
49	MYBL2	chr11:47278812-47279458	HepG2	liver:	n/a	n/a
50	CHD2	chr11:47278793-47279739	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:47278014..47279566-chr11:47397375..47399995,2	K562	blood:
2	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
3	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
4	chr11:47198598..47200151-chr11:47277071..47279146,2	K562	blood:
5	chr11:47205592..47209017-chr11:47278399..47281373,5	MCF-7	breast:
6	chr11:47198332..47200151-chr11:47277071..47279374,2	K562	blood:
7	chr11:47277336..47279783-chr11:47290576..47292976,4	MCF-7	breast:
8	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
9	chr11:47277979..47283267-chr11:47289057..47293509,9	K562	blood:
10	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000149182	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000066336	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10501321	0.98[GIH][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1052373	0.94[ASW][hapmap];0.84[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1055510	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10742799	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10742801	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10769252	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10838681	0.87[ASW][hapmap];0.86[CHB][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes]
rs10838684	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838687	0.83[MKK][hapmap]
rs10838690	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10838691	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838692	0.94[ASW][hapmap];0.84[CEU][hapmap];0.98[GIH][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838693	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11039156	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039166	0.84[CEU][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11039167	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12575456	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1375688	0.84[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1449627	0.94[ASW][hapmap];0.84[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1685404	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs2013867	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2167079	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2269434	0.88[CEU][hapmap]
rs2279239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301216	0.82[AMR][1000 genomes]
rs2957873	0.82[ASW][hapmap];0.81[CHD][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap]
rs326214	0.84[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs326222	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35879051	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3758669	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3758672	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3781621	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3781622	0.84[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3816725	0.94[ASW][hapmap];0.84[CEU][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847502	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4752822	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752824	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4752825	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4752973	0.82[ASW][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.80[YRI][hapmap]
rs4752980	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59663860	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61896050	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6485746	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7109147	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7109203	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7120118	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120957	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7124955	0.98[GIH][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7127907	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7129661	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7395581	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7940809	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs830085	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs901746	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.84[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3758673	ACP2	cis	Thyroid	GTEx
rs3758673	MADD	cis	parietal	SCAN
rs3758673	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs3758673	MADD	cis	cerebellum	SCAN
rs3758673	PACSIN3	cis	Esophagus Mucosa	GTEx
rs3758673	ACP2	cis	lymphoblastoid	seeQTL
rs3758673	TP53I11	cis	parietal	SCAN
rs3758673	MTCH2	cis	cerebellum	SCAN
rs3758673	C1QTNF4	cis	lymphoblastoid	seeQTL
rs3758673	NR1H3	cis	parietal	SCAN
rs3758673	NR1H3	cis	lymphoblastoid	seeQTL
rs3758673	ATG13	cis	cerebellum	SCAN
rs3758673	DDB2	cis	lymphoblastoid	seeQTL
rs3758673	UBA52	trans	parietal	SCAN
rs3758673	DGKZ	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271400-47279000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:47271400-47279000	Weak transcription	Fetal Brain Female	brain
4	chr11:47271400-47279000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:47271400-47279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:47271400-47281000	Weak transcription	Thymus	Thymus
7	chr11:47271400-47281200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr11:47271400-47281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:47271400-47281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:47271400-47281200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr11:47271600-47279000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:47272400-47286400	Weak transcription	Dnd41	blood
13	chr11:47275200-47279000	Enhancers	Fetal Muscle Leg	muscle
14	chr11:47275200-47279000	Enhancers	Right Atrium	heart
15	chr11:47275400-47279000	Enhancers	Placenta	Placenta
16	chr11:47275800-47279400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
18	chr11:47276600-47279600	Weak transcription	Fetal Thymus	thymus
19	chr11:47276800-47280800	Weak transcription	HSMMtube	muscle
20	chr11:47277000-47279000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:47277000-47279000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:47277000-47279000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:47277000-47279000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr11:47277000-47279000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:47277000-47279000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:47277000-47279000	Enhancers	Duodenum Mucosa	Duodenum
27	chr11:47277000-47279000	Enhancers	Fetal Intestine Small	intestine
28	chr11:47277000-47279000	Weak transcription	NH-A	brain
29	chr11:47277000-47279200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:47277000-47279200	Weak transcription	Brain Substantia Nigra	brain
31	chr11:47277000-47279400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:47277000-47282000	Weak transcription	Spleen	Spleen
33	chr11:47277200-47279000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:47277200-47279200	Weak transcription	Fetal Kidney	kidney
35	chr11:47277800-47279800	Enhancers	Stomach Mucosa	stomach
36	chr11:47278000-47279000	Enhancers	Brain Anterior Caudate	brain
37	chr11:47278000-47279000	Enhancers	Left Ventricle	heart
38	chr11:47278000-47279000	Enhancers	Pancreas	Pancrea
39	chr11:47278000-47279000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr11:47278000-47279200	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr11:47278400-47279000	Enhancers	Colon Smooth Muscle	Colon
42	chr11:47278600-47279000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr11:47278600-47279000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:47278600-47279000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:47278600-47279000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr11:47278600-47279000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr11:47278600-47279000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:47278600-47279000	Enhancers	Fetal Stomach	stomach
49	chr11:47278600-47279000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr11:47278600-47279200	Enhancers	NHDF-Ad	bronchial

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