Variant report

Variant	rs1462940
Chromosome Location	chr11:10562936-10562937
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	PML	chr11:10562385-10563048	K562	blood:	n/a	chr11:10562594-10562602
2	POLR2A	chr11:10562371-10562997	HL-60	blood:	n/a	n/a
3	TEAD4	chr11:10562476-10563120	K562	blood:	n/a	n/a
4	TBP	chr11:10562382-10563093	K562	blood:	n/a	n/a
5	MYC	chr11:10562546-10562966	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr11:10562589-10563006	K562	blood:	n/a	chr11:10562686-10562702 chr11:10562850-10562866 chr11:10562723-10562739
7	SP1	chr11:10562323-10563182	A549	lung:	n/a	chr11:10562505-10562515 chr11:10562786-10562795 chr11:10562785-10562797 chr11:10562786-10562800 chr11:10562786-10562796 chr11:10562785-10562796 chr11:10562786-10562795 chr11:10562785-10562797 chr11:10562690-10562703 chr11:10562787-10562796 chr11:10562786-10562796
8	SMARCB1	chr11:10562049-10563141	Hela-S3	cervix:	n/a	n/a
9	SRF	chr11:10562502-10563137	MCF-7	breast:	n/a	n/a
10	MAX	chr11:10562391-10563080	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:10562473-10563073	K562	blood:	n/a	n/a
12	E2F4	chr11:10561458-10563005	MCF10A-Er-Src	breast:	n/a	chr11:10562533-10562542 chr11:10562787-10562796
13	CTCF	chr11:10562709-10562990	GM10248	blood:	n/a	n/a
14	ATF3	chr11:10562445-10562989	A549	lung:	n/a	chr11:10562776-10562790 chr11:10562787-10562796 chr11:10562455-10562463
15	IRF1	chr11:10562533-10562996	K562	blood:	n/a	chr11:10562591-10562605 chr11:10562597-10562606 chr11:10562593-10562607 chr11:10562783-10562797
16	TAF1	chr11:10562360-10562969	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr11:10562308-10563140	NB4	blood:	n/a	n/a
18	TCF12	chr11:10562044-10563072	ECC-1	luminal epithelium:	n/a	n/a
19	CTCF	chr11:10562800-10562950	NB4	blood:	n/a	n/a
20	CTCF	chr11:10562800-10562950	NHLF	lung:	n/a	n/a
21	POLR2A	chr11:10562135-10563267	H1-hESC	embryonic stem cell:	n/a	n/a
22	PAX5	chr11:10562489-10563025	GM12892	blood:	n/a	chr11:10562596-10562605
23	POLR2A	chr11:10562480-10563027	HUVEC	blood vessel:	n/a	n/a
24	MYC	chr11:10562653-10562944	MCF-7	breast:	n/a	n/a
25	POLR2A	chr11:10562416-10563022	A549	lung:	n/a	n/a
26	SP1	chr11:10562429-10563142	A549	lung:	n/a	chr11:10562505-10562515 chr11:10562786-10562795 chr11:10562785-10562797 chr11:10562786-10562800 chr11:10562786-10562796 chr11:10562785-10562796 chr11:10562786-10562795 chr11:10562785-10562797 chr11:10562690-10562703 chr11:10562787-10562796 chr11:10562786-10562796
27	CTCF	chr11:10562664-10563007	GM13977	blood:	n/a	n/a
28	CTCF	chr11:10562800-10562950	HCFaa	heart:	n/a	n/a
29	POLR2A	chr11:10562336-10563131	A549	lung:	n/a	n/a
30	POLR2A	chr11:10562338-10563063	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr11:10562268-10563120	U87	brain:	n/a	n/a
32	POLR2A	chr11:10562349-10563068	MCF-7	breast:	n/a	n/a
33	POLR2A	chr11:10562434-10563045	SK-N-SH	brain:	n/a	n/a
34	POU2F2	chr11:10562477-10562992	GM12891	blood:	n/a	chr11:10562787-10562799
35	CTCF	chr11:10562702-10562969	MCF-7	breast:	n/a	n/a
36	CTCF	chr11:10562800-10562950	WI-38	lung:	n/a	n/a
37	GATA2	chr11:10562269-10563496	SH-SY5Y	brain:	n/a	n/a
38	E2F6	chr11:10562605-10563104	K562	blood:	n/a	chr11:10562787-10562796
39	JUND	chr11:10562515-10563145	A549	lung:	n/a	chr11:10562788-10562797
40	SIN3AK20	chr11:10562630-10562952	A549	lung:	n/a	n/a
41	MAX	chr11:10562696-10563331	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr11:10562654-10563006	K562	blood:	n/a	n/a
43	RCOR1	chr11:10562535-10563153	GM12878	blood:	n/a	n/a
44	MAX	chr11:10562057-10563285	A549	lung:	n/a	n/a
45	CEBPD	chr11:10562466-10562947	HepG2	liver:	n/a	n/a
46	POLR2A	chr11:10561314-10563085	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT5A	chr11:10562540-10563075	K562	blood:	n/a	chr11:10562594-10562605
48	POLR2A	chr11:10562453-10563079	Raji	blood:	n/a	n/a
49	MAFK	chr11:10562252-10563208	Hela-S3	cervix:	n/a	n/a
50	TAF1	chr11:10562061-10563080	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:10562913-10562963	HRE	kidney:	n/a
2	chr11:10562910-10562960	H1-hESC	embryonic stem cell:	embryo
3	chr11:10562913-10562963	H1-hESC	embryonic stem cell:	embryo
4	chr11:10562913-10562963	AoSMC	blood vessel:	n/a
5	chr11:10562913-10562963	HPAEpiC	pulmonary alveolar:	n/a
6	chr11:10562913-10562963	HCT-116	colon:	n/a
7	chr11:10562913-10562963	AG04449	skin:	fetal
8	chr11:10562910-10562960	NHDF-neo	bronchial:	n/a
9	chr11:10562913-10562963	BJ	skin:	n/a
10	chr11:10562913-10562963	NT2-D1	testis:	n/a
11	chr11:10562910-10562960	HEEpiC	esophagus:	n/a
12	chr11:10562913-10562963	MCF-7	breast:	n/a
13	chr11:10562910-10562960	K562	blood:	n/a
14	chr11:10562913-10562963	HCPEpiC	choroid plexus:	n/a
15	chr11:10562910-10562960	SK-N-SH_RA	brain:	n/a
16	chr11:10562913-10562963	HMEC	breast:	n/a
17	chr11:10562913-10562963	IMR90	lung:	fetal
18	chr11:10562910-10562960	HCM	heart:	n/a
19	chr11:10562910-10562960	HUVEC	blood vessel:	n/a
20	chr11:10562913-10562963	NHDF-neo	bronchial:	n/a
21	chr11:10562910-10562960	HRE	kidney:	n/a
22	chr11:10562910-10562960	SK-N-MC	brain:	n/a
23	chr11:10562913-10562963	HCF	heart:	n/a
24	chr11:10562910-10562960	HRPEpiC	eye:	n/a
25	chr11:10562910-10562960	HCF	heart:	n/a
26	chr11:10562910-10562960	GM12891	blood:	n/a
27	chr11:10562913-10562963	BE2_C	brain:	n/a
28	chr11:10562913-10562963	Hepatocyte	liver:	n/a
29	chr11:10562910-10562960	HCPEpiC	choroid plexus:	n/a
30	chr11:10562913-10562963	HRCEpiC	kidney:	n/a
31	chr11:10562913-10562963	NH-A	brain:	n/a
32	chr11:10562913-10562963	HL-60	blood:	n/a
33	chr11:10562913-10562963	NHBE	bronchial:	n/a
34	chr11:10562910-10562960	HL-60	blood:	n/a
35	chr11:10562910-10562960	HRCEpiC	kidney:	n/a
36	chr11:10562910-10562960	AG09319	gingival:	n/a
37	chr11:10562910-10562960	LNCaP	prostate:	n/a
38	chr11:10562913-10562963	PFSK-1	brain:	n/a
39	chr11:10562910-10562960	BJ	skin:	n/a
40	chr11:10562910-10562960	GM12892	blood:	n/a
41	chr11:10562913-10562963	AG09319	gingival:	n/a
42	chr11:10562910-10562960	ovcar-3	ovarian:	n/a
43	chr11:10562910-10562960	HNPCEpiC	eye:	n/a
44	chr11:10562913-10562963	Caco-2	colon:	n/a
45	chr11:10562910-10562960	AG04450	lung:	fetal
46	chr11:10562913-10562963	SK-N-SH_RA	brain:	n/a
47	chr11:10562913-10562963	ECC-1	luminal epithelium:	n/a
48	chr11:10562913-10562963	HEK293	kidney:	embryo
49	chr11:10562910-10562960	GM06990	blood:	n/a
50	chr11:10562910-10562960	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10476884..10479039-chr11:10561132..10563728,3	K562	blood:
2	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:
3	chr11:10471184..10472852-chr11:10561290..10564176,2	K562	blood:
4	chr11:10562280..10562997-chr8:144718095..144718659,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMPD3-1	chr11:10562819-10563089	ENSG00000177112.3
2	lnc-AMPD3-1	chr11:10562844-10563089	ENSG00000177112.3
3	lnc-AMPD3-1	chr11:10562670-10563089	NONHSAT017970
4	lnc-AMPD3-1	chr11:10562783-10563089	NONHSAT017971
5	lnc-AMPD3-1	chr11:10562783-10563089	NONHSAT017972
6	lnc-AMPD3-1	chr11:10562783-10563089	NONHSAT017973
7	lnc-AMPD3-1	chr11:10562783-10563089	NR_034093

Variant related genes	Relation type
RNF141	TF binding region
RNF141	CpG island
ENSG00000133805	Chromatin interaction
ENSG00000072952	Chromatin interaction
ENSG00000183309	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1035691	1.00[JPT][hapmap]
rs10840457	1.00[JPT][hapmap]
rs11042902	1.00[JPT][hapmap]
rs11603178	1.00[JPT][hapmap]
rs1346022	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1364738	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364739	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs16927077	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17318955	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17403175	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403439	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403460	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403795	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403942	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17403977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1863243	1.00[JPT][hapmap]
rs1863244	1.00[JPT][hapmap]
rs1979367	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098839	1.00[JPT][hapmap]
rs4025	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41464450	0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4442541	1.00[JPT][hapmap]
rs4909945	1.00[JPT][hapmap]
rs4910160	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910161	0.81[AMR][1000 genomes]
rs4910165	1.00[JPT][hapmap]
rs6484336	1.00[CHB][hapmap]
rs7940646	1.00[JPT][hapmap]
rs7948666	1.00[LWK][hapmap]
rs7949992	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950829	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952446	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881869	1.00[JPT][hapmap]
rs903822	1.00[JPT][hapmap]
rs903823	1.00[JPT][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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1044011	chr11:10529353-10564450	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1462940	AMPD3	cis	cerebellum	SCAN
rs1462940	RNF141	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10560800-10563200	Active TSS	Aorta	Aorta
2	chr11:10561200-10563400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:10561400-10563000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:10561400-10563200	Active TSS	Right Atrium	heart
5	chr11:10561400-10563200	Active TSS	NHDF-Ad	bronchial
6	chr11:10561400-10563400	Active TSS	Stomach Smooth Muscle	stomach
7	chr11:10561400-10563400	Active TSS	NHLF	lung
8	chr11:10561600-10563000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr11:10561600-10563000	Active TSS	Muscle Satellite Cultured Cells	--
10	chr11:10561600-10563000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:10561600-10563000	Active TSS	Left Ventricle	heart
12	chr11:10561600-10563000	Active TSS	HepG2	liver
13	chr11:10561600-10563200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:10561600-10563200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr11:10561600-10563200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:10561600-10563200	Active TSS	Colonic Mucosa	Colon
17	chr11:10561600-10563200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr11:10561600-10563200	Active TSS	Lung	lung
19	chr11:10561600-10563200	Active TSS	Placenta Amnion	Placenta Amnion
20	chr11:10561600-10563200	Active TSS	Psoas Muscle	Psoas
21	chr11:10561600-10563400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr11:10561600-10563400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:10561600-10563400	Active TSS	Esophagus	oesophagus
24	chr11:10561800-10563000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:10561800-10563000	Active TSS	Brain Cingulate Gyrus	brain
26	chr11:10561800-10563000	Active TSS	Brain Germinal Matrix	brain
27	chr11:10561800-10563000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr11:10561800-10563000	Active TSS	Brain Substantia Nigra	brain
29	chr11:10561800-10563000	Active TSS	Fetal Muscle Leg	muscle
30	chr11:10561800-10563000	Active TSS	Placenta	Placenta
31	chr11:10561800-10563000	Active TSS	Fetal Stomach	stomach
32	chr11:10561800-10563000	Active TSS	Hela-S3	cervix
33	chr11:10561800-10563000	Active TSS	K562	blood
34	chr11:10561800-10563000	Active TSS	NHEK	skin
35	chr11:10561800-10563200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:10561800-10563200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr11:10561800-10563200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:10561800-10563200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:10561800-10563200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:10561800-10563200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr11:10561800-10563200	Active TSS	Ovary	ovary
42	chr11:10561800-10563200	Active TSS	Right Ventricle	heart
43	chr11:10561800-10563200	Active TSS	A549	lung
44	chr11:10561800-10563200	Active TSS	HSMM	muscle
45	chr11:10561800-10563400	Active TSS	Brain Angular Gyrus	brain
46	chr11:10562000-10563000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:10562000-10563000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:10562000-10563000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:10562000-10563000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:10562000-10563000	Active TSS	Brain Hippocampus Middle	brain

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