Variant report

Variant	rs4486654
Chromosome Location	chr11:77300643-77300644
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	ELF1	chr11:77300275-77301715	GM12878	blood:	n/a	chr11:77300759-77300771
2	MYC	chr11:77300451-77300727	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr11:77300411-77300752	K562	blood:	n/a	n/a
4	TAF1	chr11:77300382-77300988	K562	blood:	n/a	n/a
5	SIN3AK20	chr11:77299807-77301958	MCF-7	breast:	n/a	n/a
6	TAF1	chr11:77300521-77301270	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:77300316-77301867	Hela-S3	cervix:	n/a	n/a
8	MYC	chr11:77300292-77301161	K562	blood:	n/a	n/a
9	POLR2A	chr11:77300109-77300815	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr11:77300512-77300657	GM19238	blood:	n/a	chr11:77300578-77300588
11	CTCF	chr11:77300529-77300684	Pancreas_OC	pancreas:	n/a	chr11:77300578-77300588
12	POLR2A	chr11:77300312-77301521	HL-60	blood:	n/a	n/a
13	POLR2A	chr11:77299923-77302161	HepG2	liver:	n/a	n/a
14	MAX	chr11:77300419-77301611	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:77300366-77301550	GM19193	blood:	n/a	n/a
16	TCF7L2	chr11:77299802-77301737	PANC-1	pancreas:	n/a	n/a
17	E2F4	chr11:77300643-77300722	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr11:77300421-77301157	HUVEC	blood vessel:	n/a	n/a
19	MAZ	chr11:77300380-77301118	HepG2	liver:	n/a	n/a
20	HCFC1	chr11:77300430-77301027	K562	blood:	n/a	n/a
21	CTCF	chr11:77300520-77300670	GM12871	blood:	n/a	chr11:77300578-77300588
22	MAX	chr11:77299984-77301900	MCF-7	breast:	n/a	n/a
23	POLR2A	chr11:77300308-77301717	MCF-7	breast:	n/a	n/a
24	YY1	chr11:77300307-77300752	GM12878	blood:	n/a	n/a
25	E2F6	chr11:77300350-77301664	H1-hESC	embryonic stem cell:	n/a	chr11:77300876-77300885
26	MAX	chr11:77299950-77301749	A549	lung:	n/a	n/a
27	YY1	chr11:77300179-77300656	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr11:77300521-77300775	MCF-7	breast:	n/a	chr11:77300578-77300588
29	MAX	chr11:77300089-77301531	A549	lung:	n/a	n/a
30	POLR2A	chr11:77300352-77300747	GM12892	blood:	n/a	n/a
31	FOSL2	chr11:77300328-77301201	HepG2	liver:	n/a	chr11:77300875-77300884
32	MXI1	chr11:77300088-77301665	HepG2	liver:	n/a	n/a
33	POLR2A	chr11:77300514-77300770	GM12891	blood:	n/a	n/a
34	TAF1	chr11:77300247-77300888	ECC-1	luminal epithelium:	n/a	n/a
35	ELF1	chr11:77300512-77301068	K562	blood:	n/a	chr11:77300759-77300771
36	CREB1	chr11:77300205-77301754	HepG2	liver:	n/a	n/a
37	TAF1	chr11:77300297-77301093	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr11:77300342-77301202	ECC-1	luminal epithelium:	n/a	n/a
39	ELK1	chr11:77300580-77300713	Hela-S3	cervix:	n/a	n/a
40	ZNF263	chr11:77300382-77301530	HEK293-T-REx	kidney:	n/a	n/a
41	YY1	chr11:77300358-77301595	HepG2	liver:	n/a	chr11:77300953-77300964 chr11:77300759-77300773
42	CTCF	chr11:77300500-77300650	GM12865	blood:	n/a	chr11:77300578-77300588
43	RFX5	chr11:77300448-77300703	Hela-S3	cervix:	n/a	n/a
44	E2F6	chr11:77300101-77301547	K562	blood:	n/a	chr11:77300876-77300885
45	HDAC2	chr11:77300288-77301192	HepG2	liver:	n/a	chr11:77300505-77300519 chr11:77300333-77300347
46	POLR2A	chr11:77300364-77301684	GM12892	blood:	n/a	n/a
47	RFX5	chr11:77300353-77301728	HepG2	liver:	n/a	n/a
48	CBX3	chr11:77300183-77300776	K562	blood:	n/a	n/a
49	MAX	chr11:77300190-77301447	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr11:77300234-77301721	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:77300040..77302166-chr11:77305563..77307325,2	MCF-7	breast:
2	chr11:77299407..77303220-chr11:77304055..77306866,3	MCF-7	breast:
3	chr11:77276333..77280198-chr11:77299604..77302208,3	MCF-7	breast:
4	chr11:77299067..77304108-chr11:77304115..77308042,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AQP11-3	chr11:77300436-77300725	NONHSAT023223

Variant related genes	Relation type
AQP11	TF binding region
ENSG00000238880	Chromatin interaction
ENSG00000271767	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11237234	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11822592	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12417215	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12418261	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419186	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12420021	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12421695	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12574660	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12574999	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12575305	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12575763	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12577362	0.84[ASN][1000 genomes]
rs12577552	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1540179	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1945751	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2156842	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187547	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276415	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276416	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28421376	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28730304	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3781616	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4269952	0.83[EUR][1000 genomes]
rs4301811	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4399350	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4553396	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4606503	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944169	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944170	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944171	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944173	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4945182	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945183	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945186	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4945187	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945189	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945190	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4945191	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4945192	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56175172	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57332020	0.81[EUR][1000 genomes]
rs57588070	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57805854	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58608947	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58720932	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59459776	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59581090	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59765258	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59832115	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59969402	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59983642	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60045757	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60132034	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60842160	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60849458	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60929773	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61358482	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61468764	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6592736	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66488360	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66504136	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66684353	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67062156	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67807487	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67843465	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67881763	0.84[EUR][1000 genomes]
rs68013767	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68052959	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7106659	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7109398	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7109527	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7119665	0.80[EUR][1000 genomes]
rs7119934	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7128881	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs713083	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131169	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7131298	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72943487	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72943494	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72943497	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72945524	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72945540	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72945566	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72945586	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7925252	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7930885	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7930988	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932111	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932603	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7933197	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7942838	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7947430	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7950612	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
9	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4486654	AAMDC	cis	Thyroid	GTEx
rs4486654	AAMDC	cis	Artery Tibial	GTEx
rs4486654	RP11-91P24.6	cis	Thyroid	GTEx
rs4486654	RP11-91P24.7	cis	Thyroid	GTEx
rs4486654	RSF1	Cis_1M	lymphoblastoid	RTeQTL
rs4486654	RP11-91P24.6	cis	Artery Tibial	GTEx
rs4486654	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs4486654	RP11-91P24.7	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77299600-77301000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:77299600-77301200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr11:77299600-77302000	Active TSS	Pancreas	Pancrea
4	chr11:77299800-77301000	Active TSS	Gastric	stomach
5	chr11:77299800-77301000	Active TSS	NHLF	lung
6	chr11:77299800-77301200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:77299800-77301200	Active TSS	Brain Anterior Caudate	brain
8	chr11:77299800-77301400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr11:77299800-77301400	Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr11:77299800-77301400	Active TSS	Brain Substantia Nigra	brain
11	chr11:77299800-77301400	Active TSS	Fetal Brain Female	brain
12	chr11:77299800-77301600	Active TSS	A549	lung
13	chr11:77299800-77301600	ZNF genes & repeats	Dnd41	blood
14	chr11:77299800-77301800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr11:77299800-77301800	Active TSS	Psoas Muscle	Psoas
16	chr11:77299800-77301800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr11:77299800-77301800	Active TSS	NHDF-Ad	bronchial
18	chr11:77299800-77302000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:77299800-77302400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:77299800-77302400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr11:77300000-77301200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr11:77300000-77301200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:77300000-77301200	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr11:77300000-77301200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:77300000-77301200	Active TSS	Left Ventricle	heart
26	chr11:77300000-77301200	Active TSS	Rectal Smooth Muscle	rectum
27	chr11:77300000-77301200	Active TSS	Right Ventricle	heart
28	chr11:77300000-77301200	Active TSS	HSMMtube	muscle
29	chr11:77300000-77301400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr11:77300000-77301400	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr11:77300000-77301400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:77300000-77301400	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr11:77300000-77301600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr11:77300000-77301600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr11:77300000-77301800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr11:77300000-77301800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:77300000-77301800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:77300000-77302000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr11:77300000-77302000	Active TSS	Aorta	Aorta
40	chr11:77300000-77302000	Active TSS	Fetal Kidney	kidney
41	chr11:77300200-77300800	Active TSS	Thymus	Thymus
42	chr11:77300200-77301000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:77300200-77301000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:77300200-77301000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:77300200-77301000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:77300200-77301200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:77300200-77301200	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr11:77300200-77301200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr11:77300200-77301200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr11:77300200-77301200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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