Variant report

Variant	rs4682299
Chromosome Location	chr3:111451104-111451105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr3:111450937-111452661	HepG2	liver:	n/a	n/a
2	FOXA1	chr3:111451053-111451534	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:111451020-111451543	HepG2	liver:	n/a	n/a
4	FOXA2	chr3:111451063-111451593	A549	lung:	n/a	n/a
5	FOXA2	chr3:111451073-111451445	HepG2	liver:	n/a	n/a
6	RCOR1	chr3:111451062-111451450	HepG2	liver:	n/a	n/a
7	FOXA1	chr3:111451085-111451528	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:111451065-111451695	HepG2	liver:	n/a	n/a
9	HEY1	chr3:111451050-111451589	HepG2	liver:	n/a	n/a
10	FOXA1	chr3:111451061-111451581	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:111451075-111451576	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:111451094-111453195	HepG2	liver:	n/a	n/a
13	FOXA1	chr3:111451055-111451511	T-47D	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:111451090-111451140	AG04450	lung:	fetal
2	chr3:111451090-111451140	U87	brain:	n/a
3	chr3:111451090-111451140	HRPEpiC	eye:	n/a
4	chr3:111451090-111451140	SK-N-MC	brain:	n/a
5	chr3:111451090-111451140	BJ	skin:	n/a
6	chr3:111451090-111451140	PFSK-1	brain:	n/a
7	chr3:111451090-111451140	ECC-1	luminal epithelium:	n/a
8	chr3:111451090-111451140	NH-A	brain:	n/a
9	chr3:111451090-111451140	SAEC	small airway:	n/a
10	chr3:111451090-111451140	NT2-D1	testis:	n/a
11	chr3:111451090-111451140	GM12891	blood:	n/a
12	chr3:111451090-111451140	HL-60	blood:	n/a
13	chr3:111451090-111451140	NHDF-neo	bronchial:	n/a
14	chr3:111451090-111451140	PrEC	prostate:	n/a
15	chr3:111451090-111451140	ProgFib	skin:	n/a
16	chr3:111451090-111451140	HMEC	breast:	n/a
17	chr3:111451090-111451140	SK-N-SH	brain:	n/a
18	chr3:111451090-111451140	MCF-7	breast:	n/a
19	chr3:111451090-111451140	AoSMC	blood vessel:	n/a
20	chr3:111451090-111451140	BE2_C	brain:	n/a
21	chr3:111451090-111451140	SKMC	muscle:	n/a
22	chr3:111451090-111451140	H1-hESC	embryonic stem cell:	embryo
23	chr3:111451090-111451140	MCF10A-Er-Src	breast:	n/a
24	chr3:111451090-111451140	RPTEC	kidney:	n/a
25	chr3:111451090-111451140	LNCaP	prostate:	n/a
26	chr3:111451090-111451140	AG09309	skin:	n/a
27	chr3:111451090-111451140	SK-N-SH_RA	brain:	n/a
28	chr3:111451090-111451140	AG10803	skin:	n/a
29	chr3:111451090-111451140	HEEpiC	esophagus:	n/a
30	chr3:111451090-111451140	PANC-1	pancreas:	n/a
31	chr3:111451090-111451140	CMK	blood:	n/a
32	chr3:111451090-111451140	HNPCEpiC	eye:	n/a
33	chr3:111451090-111451140	HepG2	liver:	n/a
34	chr3:111451090-111451140	T-47D	breast:	n/a
35	chr3:111451090-111451140	HCF	heart:	n/a
36	chr3:111451090-111451140	HCT-116	colon:	n/a
37	chr3:111451090-111451140	Jurkat	blood:	n/a
38	chr3:111451090-111451140	Hepatocyte	liver:	n/a
39	chr3:111451090-111451140	HAEpiC	amniotic membrane:	n/a
40	chr3:111451090-111451140	HIPEpiC	eye:	n/a
41	chr3:111451090-111451140	AG09319	gingival:	n/a
42	chr3:111451090-111451140	GM19239	blood:	n/a
43	chr3:111451090-111451140	ovcar-3	ovarian:	n/a
44	chr3:111451090-111451140	HUVEC	blood vessel:	n/a
45	chr3:111451090-111451140	GM12892	blood:	n/a
46	chr3:111451090-111451140	HEK293	kidney:	embryo
47	chr3:111451090-111451140	K562	blood:	n/a
48	chr3:111451090-111451140	IMR90	lung:	fetal
49	chr3:111451090-111451140	HPAEpiC	pulmonary alveolar:	n/a
50	chr3:111451090-111451140	HRCEpiC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111448469..111451104-chr3:111452736..111455582,2	MCF-7	breast:

No data

Variant related genes	Relation type
PLCXD2	TF binding region
PHLDB2	TF binding region
PLCXD2	CpG island
PHLDB2	CpG island

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10470303	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10804492	0.81[CHD][hapmap]
rs11710738	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11711533	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11711582	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12330761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490166	0.95[GIH][hapmap]
rs12632310	0.82[JPT][hapmap]
rs13074817	0.95[GIH][hapmap]
rs13079085	0.95[GIH][hapmap]
rs2137595	0.91[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs4284954	0.95[GIH][hapmap]
rs4401340	0.96[TSI][hapmap]
rs4413291	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs4431081	0.95[GIH][hapmap]
rs4557129	0.81[CHD][hapmap]
rs4682057	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682298	0.91[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682303	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682305	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4682312	0.88[CEU][hapmap]
rs4682314	0.82[ASW][hapmap];0.88[CEU][hapmap]
rs56028731	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62273780	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62275532	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438003	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6768713	0.95[GIH][hapmap]
rs6784753	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6786612	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6788543	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796087	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7609653	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7629156	0.81[CHD][hapmap]
rs955381	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959540	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9818574	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9823974	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9834030	0.95[GIH][hapmap]
rs9868171	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9870656	0.87[CEU][hapmap]
rs9877859	0.91[ASW][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4682299	CCDC80	cis	parietal	SCAN
rs4682299	ZBED2	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:111431600-111451400	Weak transcription	Gastric	stomach
5	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
7	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
8	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr3:111442400-111456000	Weak transcription	Lung	lung
11	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
14	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
16	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:111447200-111451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:111447800-111451200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:111448600-111451200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:111448800-111453600	Weak transcription	Right Atrium	heart
22	chr3:111448800-111454200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:111449000-111453400	Weak transcription	Fetal Heart	heart
24	chr3:111449000-111453600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:111449000-111453600	Weak transcription	HUVEC	blood vessel
26	chr3:111449000-111454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:111449200-111453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:111449200-111453600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:111449400-111451200	Weak transcription	Fetal Stomach	stomach
31	chr3:111449400-111453400	Weak transcription	HSMMtube	muscle
32	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:111449600-111452600	Weak transcription	HSMM	muscle
34	chr3:111449600-111452800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:111449600-111452800	Weak transcription	Hela-S3	cervix
36	chr3:111449600-111452800	Weak transcription	Osteobl	bone
37	chr3:111449600-111453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:111449600-111453400	Weak transcription	NH-A	brain
39	chr3:111449600-111453600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:111449600-111453800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:111449600-111453800	Weak transcription	NHLF	lung
42	chr3:111449600-111456000	Weak transcription	Esophagus	oesophagus
43	chr3:111449800-111453600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:111449800-111453600	Weak transcription	NHDF-Ad	bronchial
45	chr3:111450200-111451200	Weak transcription	Thymus	Thymus
46	chr3:111450200-111451200	Weak transcription	HMEC	breast
47	chr3:111450200-111451200	Weak transcription	NHEK	skin
48	chr3:111450200-111452800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:111450600-111451200	Enhancers	Liver	Liver
50	chr3:111450800-111451200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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