Variant report

Variant	rs4648254
Chromosome Location	chr1:186650512-186650513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:186649045-186650512	A549	lung:	n/a	chr1:186650056-186650064
2	POLR2A	chr1:186649021-186650646	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:186649009-186650813	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr1:186650380-186650530	AG04449	skin:	n/a	n/a
5	FOS	chr1:186650195-186650515	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:186647362-186650832	PBDE	blood:	n/a	n/a
7	POLR2A	chr1:186648986-186650813	Hela-S3	cervix:	n/a	n/a
8	RCOR1	chr1:186649049-186650711	Hela-S3	cervix:	n/a	n/a
9	ZKSCAN1	chr1:186649117-186650711	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:186647276-186650764	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:186648078-186651650	IMR90	lung:	n/a	n/a
12	RFX5	chr1:186648944-186650556	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:186646993-186651195	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr1:186648991-186650805	A549	lung:	n/a	n/a
15	CHD2	chr1:186649176-186650578	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr1:186648686-186651449	A549	lung:	n/a	chr1:186651134-186651142
17	TFAP2A	chr1:186649227-186650695	Hela-S3	cervix:	n/a	chr1:186650483-186650494 chr1:186649820-186649834 chr1:186649822-186649832 chr1:186650483-186650494 chr1:186650006-186650017 chr1:186649822-186649832 chr1:186649820-186649834 chr1:186649822-186649832 chr1:186650483-186650494 chr1:186650483-186650494 chr1:186650482-186650496
18	BRCA1	chr1:186650113-186652019	Hela-S3	cervix:	n/a	chr1:186650261-186650268 chr1:186651446-186651453
19	SMC3	chr1:186649044-186650714	Hela-S3	cervix:	n/a	n/a
20	STAT1	chr1:186649155-186650673	Hela-S3	cervix:	n/a	chr1:186649928-186649940 chr1:186650411-186650419 chr1:186650053-186650060
21	TAF1	chr1:186650212-186650552	Hela-S3	cervix:	n/a	n/a
22	TBP	chr1:186648845-186652253	Hela-S3	cervix:	n/a	n/a
23	MYC	chr1:186650318-186650610	MCF10A-Er-Src	breast:	n/a	n/a
24	TFAP2C	chr1:186649202-186650699	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:186648899-186650975	MCF10A-Er-Src	breast:	n/a	n/a
26	MXI1	chr1:186649054-186650718	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:186647207-186651362	Hela-S3	cervix:	n/a	n/a
28	STAT3	chr1:186650374-186650720	MCF10A-Er-Src	breast:	n/a	chr1:186650411-186650419
29	MAFK	chr1:186649077-186650545	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:186649177-186650588	Hela-S3	cervix:	n/a	n/a
31	MAX	chr1:186649107-186650735	Hela-S3	cervix:	n/a	chr1:186650056-186650064

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:186650479-186650529	SK-N-SH	brain:	n/a
2	chr1:186650479-186650529	Caco-2	colon:	n/a
3	chr1:186650479-186650529	NHBE	bronchial:	n/a
4	chr1:186650479-186650529	Jurkat	blood:	n/a
5	chr1:186650479-186650529	ProgFib	skin:	n/a
6	chr1:186650479-186650529	T-47D	breast:	n/a
7	chr1:186650479-186650529	GM12878	blood:	n/a
8	chr1:186650479-186650529	Hepatocyte	liver:	n/a
9	chr1:186650479-186650529	NT2-D1	testis:	n/a
10	chr1:186650479-186650529	HCPEpiC	choroid plexus:	n/a
11	chr1:186650479-186650529	CMK	blood:	n/a
12	chr1:186650479-186650529	MCF-7	breast:	n/a
13	chr1:186650479-186650529	AoSMC	blood vessel:	n/a
14	chr1:186650479-186650529	HRPEpiC	eye:	n/a
15	chr1:186650479-186650529	NHDF-neo	bronchial:	n/a
16	chr1:186650479-186650529	PrEC	prostate:	n/a
17	chr1:186650479-186650529	AG10803	skin:	n/a
18	chr1:186650479-186650529	RPTEC	kidney:	n/a
19	chr1:186650479-186650529	HepG2	liver:	n/a
20	chr1:186650479-186650529	HPAEpiC	pulmonary alveolar:	n/a
21	chr1:186650479-186650529	LNCaP	prostate:	n/a
22	chr1:186650479-186650529	BE2_C	brain:	n/a
23	chr1:186650479-186650529	AG09319	gingival:	n/a
24	chr1:186650479-186650529	HL-60	blood:	n/a
25	chr1:186650479-186650529	Hela-S3	cervix:	n/a
26	chr1:186650479-186650529	GM19239	blood:	n/a
27	chr1:186650479-186650529	HNPCEpiC	eye:	n/a
28	chr1:186650479-186650529	AG04450	lung:	fetal
29	chr1:186650479-186650529	HCF	heart:	n/a
30	chr1:186650479-186650529	HCM	heart:	n/a
31	chr1:186650479-186650529	MCF10A-Er-Src	breast:	n/a
32	chr1:186650479-186650529	BJ	skin:	n/a
33	chr1:186650479-186650529	PANC-1	pancreas:	n/a
34	chr1:186650479-186650529	GM06990	blood:	n/a
35	chr1:186650479-186650529	K562	blood:	n/a
36	chr1:186650479-186650529	GM12892	blood:	n/a
37	chr1:186650479-186650529	HRE	kidney:	n/a
38	chr1:186650479-186650529	HRCEpiC	kidney:	n/a
39	chr1:186650479-186650529	HEK293	kidney:	embryo
40	chr1:186650479-186650529	A549	lung:	n/a
41	chr1:186650479-186650529	SKMC	muscle:	n/a
42	chr1:186650479-186650529	HMEC	breast:	n/a
43	chr1:186650479-186650529	HAEpiC	amniotic membrane:	n/a
44	chr1:186650479-186650529	GM12891	blood:	n/a
45	chr1:186650479-186650529	ECC-1	luminal epithelium:	n/a
46	chr1:186650479-186650529	PFSK-1	brain:	n/a
47	chr1:186650479-186650529	HEEpiC	esophagus:	n/a
48	chr1:186650479-186650529	HCT-116	colon:	n/a
49	chr1:186650479-186650529	U87	brain:	n/a
50	chr1:186650479-186650529	HUVEC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
2	chr1:186650209..186651033-chr6:89789993..89790875,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLA2G4A-10	chr1:186649754-186650578	ENSG00000273129.1

No data

Variant related genes	Relation type
PTGS2	TF binding region
PTGS2	CpG island
ENSG00000271931	Chromatin interaction
ENSG00000146278	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4648301	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186646400-186651000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:186647000-186652000	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:186647600-186651000	Active TSS	A549	lung
4	chr1:186647800-186651800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:186648000-186651200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:186648000-186651600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:186648000-186651800	Active TSS	Colon Smooth Muscle	Colon
8	chr1:186648000-186651800	Active TSS	NHDF-Ad	bronchial
9	chr1:186648200-186650600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:186648200-186651000	Active TSS	Fetal Stomach	stomach
11	chr1:186648200-186651000	Active TSS	Osteobl	bone
12	chr1:186648200-186651200	Active TSS	NH-A	brain
13	chr1:186648400-186650800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:186648400-186650800	Active TSS	Colonic Mucosa	Colon
15	chr1:186648400-186650800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
16	chr1:186648400-186651000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:186648400-186652000	Active TSS	Right Atrium	heart
18	chr1:186648600-186651000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:186648600-186651200	Active TSS	Hela-S3	cervix
20	chr1:186648600-186651400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:186648600-186651400	Active TSS	NHLF	lung
22	chr1:186648600-186651600	Active TSS	HMEC	breast
23	chr1:186648600-186651800	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:186648600-186652000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:186648600-186652000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:186648600-186652400	Active TSS	NHEK	skin
27	chr1:186648800-186650600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:186648800-186650800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:186648800-186650800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr1:186648800-186650800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:186648800-186650800	Active TSS	Duodenum Mucosa	Duodenum
32	chr1:186648800-186650800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
33	chr1:186649000-186650600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr1:186649000-186650600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr1:186649000-186650600	Active TSS	H9 Cell Line	embryonic stem cell
36	chr1:186649000-186650600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:186649000-186650600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr1:186649000-186650600	Active TSS	Brain Anterior Caudate	brain
39	chr1:186649000-186650600	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr1:186649000-186650600	Active TSS	Ovary	ovary
41	chr1:186649000-186650600	Active TSS	Right Ventricle	heart
42	chr1:186649000-186650800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:186649000-186650800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:186649000-186650800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:186649000-186650800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:186649000-186650800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
47	chr1:186649000-186650800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:186649000-186650800	Active TSS	Brain Cingulate Gyrus	brain
49	chr1:186649200-186650600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
50	chr1:186649200-186651200	Active TSS	Aorta	Aorta

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