Variant report

Variant	rs4855883
Chromosome Location	chr3:49711314-49711315
allele	C/G
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	POLR2A	chr3:49710639-49712148	GM18526	blood:	n/a	n/a
2	TEAD4	chr3:49711094-49711569	H1-hESC	embryonic stem cell:	n/a	chr3:49711289-49711298
3	CEBPD	chr3:49710983-49711768	HepG2	liver:	n/a	n/a
4	MAX	chr3:49710499-49712438	ECC-1	luminal epithelium:	n/a	chr3:49710764-49710774 chr3:49710765-49710772 chr3:49712213-49712223 chr3:49710763-49710774 chr3:49710762-49710777 chr3:49710764-49710773
5	CTCF	chr3:49711260-49711410	HBMEC	blood vessel:	n/a	n/a
6	MYC	chr3:49711176-49711536	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:49710420-49713358	K562	blood:	n/a	n/a
8	POLR2A	chr3:49710568-49712691	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49711038-49712032	A549	lung:	n/a	n/a
10	ELF1	chr3:49710985-49712151	MCF-7	breast:	n/a	chr3:49711784-49711793 chr3:49711783-49711794 chr3:49711205-49711217
11	TRIM28	chr3:49711205-49711593	K562	blood:	n/a	n/a
12	BHLHE40	chr3:49710768-49712484	K562	blood:	n/a	chr3:49711202-49711218
13	TAF1	chr3:49710761-49712150	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F4	chr3:49711055-49711432	GM12878	blood:	n/a	n/a
15	MAX	chr3:49710446-49712549	HCT-116	colon:	n/a	chr3:49710764-49710774 chr3:49710765-49710772 chr3:49712213-49712223 chr3:49710763-49710774 chr3:49710762-49710777 chr3:49710764-49710773
16	PAX5	chr3:49711013-49712002	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:49710892-49712191	U87	brain:	n/a	n/a
18	EGR1	chr3:49711158-49711824	GM12878	blood:	n/a	chr3:49711570-49711580 chr3:49711571-49711581 chr3:49711766-49711779 chr3:49711761-49711783 chr3:49711783-49711792
19	POLR2A	chr3:49710549-49712002	HepG2	liver:	n/a	n/a
20	BHLHE40	chr3:49710791-49711918	GM12878	blood:	n/a	chr3:49711202-49711218
21	MYC	chr3:49710974-49711664	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:49710718-49712064	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:49710634-49712223	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:49710991-49712177	GM12878	blood:	n/a	n/a
25	CHD2	chr3:49710760-49712326	Hela-S3	cervix:	n/a	chr3:49712219-49712229
26	POLR2A	chr3:49710565-49712191	K562	blood:	n/a	n/a
27	TEAD4	chr3:49711120-49711419	HepG2	liver:	n/a	chr3:49711289-49711298
28	ZNF143	chr3:49711100-49711918	GM12878	blood:	n/a	n/a
29	TAF1	chr3:49710581-49712222	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:49710567-49712058	GM12891	blood:	n/a	n/a
31	ZMIZ1	chr3:49710986-49711804	K562	blood:	n/a	n/a
32	TCF7L2	chr3:49711097-49712014	HCT-116	colon:	n/a	n/a
33	POLR2A	chr3:49710585-49712418	HepG2	liver:	n/a	n/a
34	GABPA	chr3:49711054-49712033	HL-60	blood:	n/a	chr3:49711571-49711580
35	YY1	chr3:49711146-49711556	HCT-116	colon:	n/a	n/a
36	SMARCB1	chr3:49710645-49712688	Hela-S3	cervix:	n/a	n/a
37	TCF3	chr3:49711280-49711621	GM12878	blood:	n/a	n/a
38	TFAP2C	chr3:49710776-49712344	Hela-S3	cervix:	n/a	chr3:49711720-49711735
39	POLR2A	chr3:49710612-49712068	GM12891	blood:	n/a	n/a
40	TAF1	chr3:49711297-49711582	GM12892	blood:	n/a	n/a
41	CREB1	chr3:49710551-49712452	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:49710926-49712051	HEK293	kidney:	n/a	n/a
43	MXI1	chr3:49711030-49712128	K562	blood:	n/a	n/a
44	ZBTB7A	chr3:49711259-49711766	K562	blood:	n/a	n/a
45	MAX	chr3:49710543-49712359	HepG2	liver:	n/a	chr3:49710764-49710774 chr3:49710765-49710772 chr3:49712213-49712223 chr3:49710763-49710774 chr3:49710762-49710777 chr3:49710764-49710773
46	POU2F2	chr3:49711005-49711611	GM12891	blood:	n/a	n/a
47	POLR2A	chr3:49710596-49712085	GM12892	blood:	n/a	n/a
48	TFAP2A	chr3:49710932-49712334	Hela-S3	cervix:	n/a	chr3:49711103-49711115 chr3:49711724-49711735 chr3:49711557-49711572 chr3:49711103-49711115 chr3:49711724-49711735 chr3:49711363-49711371 chr3:49711724-49711735 chr3:49711720-49711735 chr3:49711103-49711115 chr3:49711724-49711735
49	PBX3	chr3:49711019-49712080	SK-N-SH	brain:	n/a	chr3:49711696-49711716 chr3:49711347-49711356
50	POLR2A	chr3:49710566-49712186	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49711283-49711333	HMEC	breast:	n/a
2	chr3:49711283-49711333	H1-hESC	embryonic stem cell:	embryo
3	chr3:49711283-49711333	MCF-7	breast:	n/a
4	chr3:49711283-49711333	NHBE	bronchial:	n/a
5	chr3:49711283-49711333	HRE	kidney:	n/a
6	chr3:49711283-49711333	HAEpiC	amniotic membrane:	n/a
7	chr3:49711283-49711333	GM12892	blood:	n/a
8	chr3:49711283-49711333	A549	lung:	n/a
9	chr3:49711283-49711333	HCF	heart:	n/a
10	chr3:49711283-49711333	HRCEpiC	kidney:	n/a
11	chr3:49711283-49711333	HPAEpiC	pulmonary alveolar:	n/a
12	chr3:49711283-49711333	K562	blood:	n/a
13	chr3:49711283-49711333	NHDF-neo	bronchial:	n/a
14	chr3:49711283-49711333	GM06990	blood:	n/a
15	chr3:49711283-49711333	NB4	blood:	n/a
16	chr3:49711283-49711333	AoSMC	blood vessel:	n/a
17	chr3:49711283-49711333	ECC-1	luminal epithelium:	n/a
18	chr3:49711283-49711333	GM19239	blood:	n/a
19	chr3:49711283-49711333	BE2_C	brain:	n/a
20	chr3:49711283-49711333	SAEC	small airway:	n/a
21	chr3:49711283-49711333	HCPEpiC	choroid plexus:	n/a
22	chr3:49711283-49711333	SKMC	muscle:	n/a
23	chr3:49711283-49711333	CMK	blood:	n/a
24	chr3:49711283-49711333	HEK293	kidney:	embryo
25	chr3:49711283-49711333	HUVEC	blood vessel:	n/a
26	chr3:49711283-49711333	AG09309	skin:	n/a
27	chr3:49711283-49711333	AG10803	skin:	n/a
28	chr3:49711283-49711333	PFSK-1	brain:	n/a
29	chr3:49711283-49711333	HepG2	liver:	n/a
30	chr3:49711283-49711333	GM12878	blood:	n/a
31	chr3:49711283-49711333	RPTEC	kidney:	n/a
32	chr3:49711283-49711333	NH-A	brain:	n/a
33	chr3:49711283-49711333	GM12891	blood:	n/a
34	chr3:49711283-49711333	IMR90	lung:	fetal
35	chr3:49711283-49711333	SK-N-MC	brain:	n/a
36	chr3:49711283-49711333	MCF10A-Er-Src	breast:	n/a
37	chr3:49711283-49711333	Caco-2	colon:	n/a
38	chr3:49711283-49711333	AG09319	gingival:	n/a
39	chr3:49711283-49711333	HNPCEpiC	eye:	n/a
40	chr3:49711283-49711333	Jurkat	blood:	n/a
41	chr3:49711283-49711333	AG04449	skin:	fetal
42	chr3:49711283-49711333	ProgFib	skin:	n/a
43	chr3:49711283-49711333	HL-60	blood:	n/a
44	chr3:49711283-49711333	HEEpiC	esophagus:	n/a
45	chr3:49711283-49711333	ovcar-3	ovarian:	n/a
46	chr3:49711283-49711333	HRPEpiC	eye:	n/a
47	chr3:49711283-49711333	PrEC	prostate:	n/a
48	chr3:49711283-49711333	U87	brain:	n/a
49	chr3:49711283-49711333	NT2-D1	testis:	n/a
50	chr3:49711283-49711333	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:103498192..103498714-chr3:49710955..49711845,2	NB4	blood:
2	chr3:49575867..49578786-chr3:49708422..49711347,4	K562	blood:
3	chr10:75006614..75007608-chr3:49711149..49711793,2	Hela-S3	cervix:
4	chr13:37574290..37574876-chr3:49710833..49711802,2	NB4	blood:
5	chr3:49709764..49714141-chr3:49724462..49728582,8	MCF-7	breast:
6	chr3:49064195..49067148-chr3:49710210..49713126,3	MCF-7	breast:
7	chr3:49709585..49712525-chr3:49736619..49738353,2	K562	blood:
8	chr3:49590547..49592695-chr3:49709214..49711684,3	MCF-7	breast:
9	chr3:49710956..49711617-chr5:96038346..96038890,2	Hela-S3	cervix:
10	chr3:49506444..49509653-chr3:49710909..49714606,3	K562	blood:
11	chr15:55488699..55489437-chr3:49710788..49711819,3	Hela-S3	cervix:
12	chr3:49710197..49713072-chr3:49759630..49762760,3	MCF-7	breast:
13	chr3:49710951..49711807-chr4:164415712..164416255,2	Hela-S3	cervix:
14	chr19:3762410..3763171-chr3:49711111..49711616,2	Hela-S3	cervix:
15	chr3:49711183..49713399-chr3:49759820..49761645,3	K562	blood:
16	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
17	chr3:49208330..49210147-chr3:49711158..49712878,2	K562	blood:
18	chr3:49447135..49449560-chr3:49709671..49711727,2	K562	blood:
19	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
20	chr1:201475614..201476476-chr3:49710954..49711674,2	Hela-S3	cervix:
21	chr3:49687205..49689854-chr3:49709727..49711348,2	MCF-7	breast:
22	chr12:56360287..56361178-chr3:49711127..49711777,2	Hela-S3	cervix:
23	chr3:49505441..49508480-chr3:49710122..49713377,5	MCF-7	breast:
24	chr3:49043665..49045561-chr3:49710277..49712167,2	K562	blood:
25	chr3:49449662..49452069-chr3:49709335..49712259,2	K562	blood:
26	chr3:49709088..49712884-chr3:49714614..49717582,5	MCF-7	breast:
27	chr3:49711233..49713399-chr3:49759820..49762894,3	K562	blood:
28	chr1:145382677..145383459-chr3:49710832..49711420,2	Hela-S3	cervix:
29	chr3:49708866..49715375-chr3:49724746..49730407,6	K562	blood:

Variant related genes	Relation type
APEH	TF binding region
APEH	CpG island
ENSG00000120697	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000137876	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000120699	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000226913	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000198498	Chromatin interaction
ENSG00000159176	Chromatin interaction
ENSG00000134899	Chromatin interaction
ENSG00000164061	Chromatin interaction
ENSG00000259970	Chromatin interaction
ENSG00000236756	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000173531	Chromatin interaction
ENSG00000183617	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000224536	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1060962	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130212	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11130213	0.91[ASN][1000 genomes]
rs1131095	0.81[ASN][1000 genomes]
rs11718165	0.85[ASN][1000 genomes]
rs11919311	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12490267	0.83[EUR][1000 genomes]
rs12497288	0.85[EUR][1000 genomes]
rs13085791	0.81[ASN][1000 genomes]
rs1352890	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1873626	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2005557	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131104	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131109	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2329020	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2960548	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3197999	0.81[ASN][1000 genomes]
rs35007338	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35404120	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855835	0.81[AMR][1000 genomes]
rs4855847	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855852	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4855881	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855884	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765869	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767878	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9822268	0.81[ASN][1000 genomes]
rs9823546	0.85[ASN][1000 genomes]
rs9836291	0.85[ASN][1000 genomes]
rs9837520	0.81[ASN][1000 genomes]
rs9858542	0.85[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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49710400-49711400	Enhancers	Fetal Heart	heart
2	chr3:49710400-49712400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49710600-49711400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr3:49710600-49711400	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr3:49710600-49711400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr3:49710600-49711400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:49710600-49711400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr3:49710600-49711400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:49710600-49711400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:49710600-49711400	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr3:49710600-49711400	Flanking Active TSS	Placenta	Placenta
12	chr3:49710600-49711400	Flanking Active TSS	Fetal Stomach	stomach
13	chr3:49710600-49711400	Flanking Active TSS	Right Ventricle	heart
14	chr3:49710600-49711400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:49710600-49711400	Flanking Active TSS	Spleen	Spleen
16	chr3:49710600-49711400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:49710600-49711600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr3:49710600-49712200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:49710600-49712200	Active TSS	Brain Hippocampus Middle	brain
20	chr3:49710600-49712400	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:49710600-49712400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:49710600-49712400	Active TSS	Colon Smooth Muscle	Colon
23	chr3:49710600-49712400	Active TSS	NHLF	lung
24	chr3:49710600-49712600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:49710600-49712600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:49710600-49712600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:49710600-49712800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:49710600-49713000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr3:49710600-49713000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:49710800-49711400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr3:49710800-49711400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:49710800-49711400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:49710800-49711400	Transcr. at gene 5' and 3'	Right Atrium	heart
34	chr3:49710800-49712200	Active TSS	Brain Angular Gyrus	brain
35	chr3:49710800-49712200	Active TSS	Brain Substantia Nigra	brain
36	chr3:49710800-49712400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:49710800-49712400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr3:49710800-49712400	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr3:49710800-49712400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:49710800-49712400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:49710800-49712400	Active TSS	Aorta	Aorta
42	chr3:49710800-49712400	Active TSS	Gastric	stomach
43	chr3:49710800-49712400	Active TSS	A549	lung
44	chr3:49710800-49712600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:49711000-49711800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:49711000-49712000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:49711000-49712000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:49711000-49712000	Active TSS	HMEC	breast
49	chr3:49711000-49712200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr3:49711000-49712200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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