Variant report

Variant	rs540857
Chromosome Location	chr11:120078890-120078891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr11:120078644-120079034	SH-SY5Y	brain:	n/a	n/a
2	CTCF	chr11:120078860-120079010	HUVEC	blood vessel:	n/a	n/a
3	EP300	chr11:120078638-120079003	K562	blood:	n/a	n/a
4	CEBPB	chr11:120078343-120079190	HepG2	liver:	n/a	n/a
5	SP1	chr11:120078679-120079121	HepG2	liver:	n/a	n/a
6	HNF4G	chr11:120078692-120079090	HepG2	liver:	n/a	n/a
7	CEBPB	chr11:120078734-120078890	K562	blood:	n/a	n/a
8	CEBPB	chr11:120078802-120079091	IMR90	lung:	n/a	n/a
9	RFX5	chr11:120078884-120079065	HepG2	liver:	n/a	n/a
10	GATA3	chr11:120078744-120079008	SH-SY5Y	brain:	n/a	n/a
11	CEBPD	chr11:120078831-120079102	HepG2	liver:	n/a	n/a
12	EP300	chr11:120078560-120079209	HepG2	liver:	n/a	n/a
13	USF2	chr11:120078842-120079050	HepG2	liver:	n/a	n/a
14	MYC	chr11:120078285-120079942	NB4	blood:	n/a	chr11:120079701-120079710
15	CTCF	chr11:120078740-120078890	SK-N-SH_RA	brain:	n/a	n/a
16	CHD2	chr11:120078775-120078998	HepG2	liver:	n/a	n/a
17	HDAC2	chr11:120078637-120079154	HepG2	liver:	n/a	n/a
18	TCF7L2	chr11:120078410-120079051	HepG2	liver:	n/a	n/a
19	CEBPB	chr11:120078711-120079192	HepG2	liver:	n/a	n/a
20	ARID3A	chr11:120078747-120079772	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:120078837-120078921	HepG2	liver:	n/a	n/a
22	EP300	chr11:120078686-120079133	HepG2	liver:	n/a	n/a
23	FOXA2	chr11:120078670-120079104	HepG2	liver:	n/a	n/a
24	SMC3	chr11:120078665-120079096	HepG2	liver:	n/a	n/a
25	MYBL2	chr11:120078637-120079203	HepG2	liver:	n/a	n/a
26	MAX	chr11:120078322-120079958	NB4	blood:	n/a	chr11:120079701-120079710
27	EP300	chr11:120078713-120079203	HepG2	liver:	n/a	n/a
28	TBP	chr11:120078507-120079073	HepG2	liver:	n/a	n/a
29	RAD21	chr11:120078712-120079060	HepG2	liver:	n/a	n/a
30	CEBPB	chr11:120078202-120079215	HepG2	liver:	n/a	n/a
31	RCOR1	chr11:120078654-120078986	HepG2	liver:	n/a	n/a
32	CEBPB	chr11:120078698-120079107	HepG2	liver:	n/a	n/a
33	MYC	chr11:120078737-120079002	HepG2	liver:	n/a	n/a
34	POLR2A	chr11:120078739-120079145	HepG2	liver:	n/a	n/a
35	MYBL2	chr11:120078448-120079163	HepG2	liver:	n/a	n/a
36	HDAC2	chr11:120078594-120079184	HepG2	liver:	n/a	n/a
37	MAX	chr11:120078713-120078937	HepG2	liver:	n/a	n/a
38	CEBPB	chr11:120078206-120079131	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:120078840-120078890	HCPEpiC	choroid plexus:	n/a
2	chr11:120078840-120078890	PANC-1	pancreas:	n/a
3	chr11:120078840-120078890	ovcar-3	ovarian:	n/a
4	chr11:120078840-120078890	BE2_C	brain:	n/a
5	chr11:120078840-120078890	HNPCEpiC	eye:	n/a
6	chr11:120078840-120078890	HCM	heart:	n/a
7	chr11:120078840-120078890	GM12892	blood:	n/a
8	chr11:120078840-120078890	HCF	heart:	n/a
9	chr11:120078840-120078890	GM19239	blood:	n/a
10	chr11:120078840-120078890	Hela-S3	cervix:	n/a
11	chr11:120078840-120078890	Jurkat	blood:	n/a
12	chr11:120078840-120078890	HPAEpiC	pulmonary alveolar:	n/a
13	chr11:120078840-120078890	NB4	blood:	n/a
14	chr11:120078840-120078890	HIPEpiC	eye:	n/a
15	chr11:120078840-120078890	HAEpiC	amniotic membrane:	n/a
16	chr11:120078840-120078890	HL-60	blood:	n/a
17	chr11:120078840-120078890	U87	brain:	n/a
18	chr11:120078840-120078890	IMR90	lung:	fetal
19	chr11:120078840-120078890	HCT-116	colon:	n/a
20	chr11:120078840-120078890	SKMC	muscle:	n/a
21	chr11:120078840-120078890	BJ	skin:	n/a
22	chr11:120078840-120078890	NHBE	bronchial:	n/a
23	chr11:120078840-120078890	HRCEpiC	kidney:	n/a
24	chr11:120078840-120078890	ECC-1	luminal epithelium:	n/a
25	chr11:120078840-120078890	GM06990	blood:	n/a
26	chr11:120078840-120078890	PrEC	prostate:	n/a
27	chr11:120078840-120078890	K562	blood:	n/a
28	chr11:120078840-120078890	NHDF-neo	bronchial:	n/a
29	chr11:120078840-120078890	SAEC	small airway:	n/a
30	chr11:120078840-120078890	MCF-7	breast:	n/a
31	chr11:120078840-120078890	HepG2	liver:	n/a
32	chr11:120078840-120078890	RPTEC	kidney:	n/a
33	chr11:120078840-120078890	AG09319	gingival:	n/a
34	chr11:120078840-120078890	HEK293	kidney:	embryo
35	chr11:120078840-120078890	H1-hESC	embryonic stem cell:	embryo
36	chr11:120078840-120078890	SK-N-SH_RA	brain:	n/a
37	chr11:120078840-120078890	SK-N-MC	brain:	n/a
38	chr11:120078840-120078890	SK-N-SH	brain:	n/a
39	chr11:120078840-120078890	HRE	kidney:	n/a
40	chr11:120078840-120078890	AoSMC	blood vessel:	n/a
41	chr11:120078840-120078890	AG10803	skin:	n/a
42	chr11:120078840-120078890	AG09309	skin:	n/a
43	chr11:120078840-120078890	NH-A	brain:	n/a
44	chr11:120078840-120078890	HEEpiC	esophagus:	n/a
45	chr11:120078840-120078890	ProgFib	skin:	n/a
46	chr11:120078840-120078890	PFSK-1	brain:	n/a
47	chr11:120078840-120078890	HRPEpiC	eye:	n/a
48	chr11:120078840-120078890	LNCaP	prostate:	n/a
49	chr11:120078840-120078890	HMEC	breast:	n/a
50	chr11:120078840-120078890	HUVEC	blood vessel:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120061784..120063825-chr11:120078138..120080529,2	K562	blood:
2	chr11:120076442..120079107-chr11:120106498..120108828,2	K562	blood:
3	chr11:120078701..120081046-chr11:120081423..120083396,2	K562	blood:

No data

Variant related genes	Relation type
OAF	TF binding region
OAF	CpG island
ENSG00000137709	Chromatin interaction
ENSG00000184232	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1287393	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1287395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253006	0.92[EUR][1000 genomes]
rs2444241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2444242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2508496	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2509623	0.92[EUR][1000 genomes]
rs2845702	0.86[EUR][1000 genomes]
rs2845708	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2847499	0.87[EUR][1000 genomes]
rs476809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs477863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs489454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs492275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513944	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs521841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs536743	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537907	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs562966	0.99[ASN][1000 genomes]
rs896695	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120074600-120079400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:120075200-120081000	Enhancers	Pancreas	Pancrea
3	chr11:120076200-120080600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:120076200-120080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:120076400-120079400	Weak transcription	NH-A	brain
6	chr11:120076600-120080600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:120076800-120079000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:120076800-120079200	Weak transcription	NHEK	skin
9	chr11:120077000-120080600	Enhancers	Fetal Stomach	stomach
10	chr11:120077000-120080800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:120077600-120079000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:120078000-120081200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr11:120078200-120079400	Enhancers	Fetal Lung	lung
14	chr11:120078200-120079400	Enhancers	Fetal Thymus	thymus
15	chr11:120078200-120080800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:120078200-120080800	Enhancers	Spleen	Spleen
17	chr11:120078400-120079200	Enhancers	Brain Germinal Matrix	brain
18	chr11:120078400-120079400	Enhancers	Fetal Heart	heart
19	chr11:120078400-120079800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:120078400-120079800	Flanking Active TSS	HepG2	liver
21	chr11:120078400-120080000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:120078400-120080000	Enhancers	Brain Substantia Nigra	brain
23	chr11:120078400-120080000	Enhancers	Left Ventricle	heart
24	chr11:120078400-120080400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:120078400-120080400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr11:120078400-120080600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:120078400-120080600	Enhancers	Adipose Nuclei	Adipose
28	chr11:120078400-120080600	Enhancers	Brain Anterior Caudate	brain
29	chr11:120078400-120080600	Enhancers	Brain Hippocampus Middle	brain
30	chr11:120078400-120080600	Enhancers	Colonic Mucosa	Colon
31	chr11:120078400-120080600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr11:120078400-120080600	Enhancers	NHDF-Ad	bronchial
33	chr11:120078400-120080800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:120078400-120080800	Enhancers	Brain Angular Gyrus	brain
35	chr11:120078400-120080800	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:120078400-120080800	Enhancers	Fetal Intestine Small	intestine
37	chr11:120078400-120080800	Enhancers	Fetal Muscle Trunk	muscle
38	chr11:120078400-120080800	Enhancers	Ovary	ovary
39	chr11:120078400-120081000	Enhancers	Esophagus	oesophagus
40	chr11:120078400-120081000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr11:120078400-120081000	Enhancers	Small Intestine	intestine
42	chr11:120078600-120079200	Enhancers	Psoas Muscle	Psoas
43	chr11:120078600-120079200	Enhancers	K562	blood
44	chr11:120078600-120079400	Enhancers	Right Ventricle	heart
45	chr11:120078600-120079600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr11:120078600-120079600	Flanking Active TSS	Liver	Liver
47	chr11:120078600-120079800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
48	chr11:120078600-120079800	Enhancers	Osteobl	bone
49	chr11:120078600-120080400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:120078600-120080400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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