Variant report

Variant	rs4682228
Chromosome Location	chr3:110791113-110791114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMARCC1	chr3:110790902-110791818	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:110788902-110792346	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:110789738-110791402	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:110788638-110791793	H1-neurons	neurons:	n/a	n/a
5	CREB1	chr3:110789883-110791675	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:110789774-110791712	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr3:110789749-110791188	SK-N-SH	brain:	n/a	n/a
8	CREB1	chr3:110791092-110791388	A549	lung:	n/a	n/a
9	E2F6	chr3:110790831-110791782	H1-hESC	embryonic stem cell:	n/a	chr3:110790904-110790912 chr3:110791076-110791086
10	CHD1	chr3:110788894-110792602	IMR90	lung:	n/a	chr3:110790569-110790579 chr3:110791180-110791190
11	POLR2A	chr3:110789680-110791135	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr3:110790842-110791310	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:110791049-110791350	Hela-S3	cervix:	n/a	n/a
14	MAZ	chr3:110789965-110791423	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:110790900-110791135	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:110789848-110791539	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:110791065-110791212	MCF10A-Er-Src	breast:	n/a	n/a
18	MXI1	chr3:110789050-110791341	HepG2	liver:	n/a	n/a
19	SIN3A	chr3:110788772-110791820	H1-hESC	embryonic stem cell:	n/a	chr3:110789838-110789851
20	E2F6	chr3:110790840-110791595	H1-hESC	embryonic stem cell:	n/a	chr3:110790904-110790912 chr3:110791076-110791086
21	JUND	chr3:110789104-110791395	SK-N-SH	brain:	n/a	n/a
22	TAF1	chr3:110790846-110791385	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:110789802-110791746	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:110789294-110791241	HepG2	liver:	n/a	n/a
25	MAX	chr3:110790844-110791460	SK-N-SH	brain:	n/a	n/a
26	MAX	chr3:110789781-110791902	Hela-S3	cervix:	n/a	n/a
27	MAX	chr3:110789270-110791983	A549	lung:	n/a	chr3:110789520-110789530
28	CHD1	chr3:110791012-110791901	H1-hESC	embryonic stem cell:	n/a	chr3:110791180-110791190
29	MAX	chr3:110791098-110791695	HepG2	liver:	n/a	n/a
30	RAD21	chr3:110788763-110792538	IMR90	lung:	n/a	n/a
31	MAX	chr3:110791113-110791928	ECC-1	luminal epithelium:	n/a	n/a
32	RCOR1	chr3:110790918-110791712	Hela-S3	cervix:	n/a	n/a
33	YY1	chr3:110790826-110791483	HepG2	liver:	n/a	chr3:110791076-110791090 chr3:110791039-110791050 chr3:110791081-110791090 chr3:110791079-110791093 chr3:110791170-110791184
34	MYC	chr3:110790975-110791203	MCF10A-Er-Src	breast:	n/a	n/a
35	RAD21	chr3:110790594-110791470	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr3:110789085-110791581	HepG2	liver:	n/a	chr3:110789520-110789530
37	TAF1	chr3:110789803-110791384	ECC-1	luminal epithelium:	n/a	n/a
38	MXI1	chr3:110788792-110792832	IMR90	lung:	n/a	n/a
39	SMC3	chr3:110790987-110791875	Hela-S3	cervix:	n/a	n/a
40	CHD2	chr3:110790109-110791497	Hela-S3	cervix:	n/a	chr3:110790569-110790579 chr3:110791180-110791190
41	POLR2A	chr3:110789748-110791453	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr3:110789764-110791350	HCT-116	colon:	n/a	n/a
43	POLR2A	chr3:110791065-110791115	MCF-7	breast:	n/a	n/a
44	CEBPB	chr3:110791025-110791828	Hela-S3	cervix:	n/a	n/a
45	MAX	chr3:110791109-110791634	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr3:110789082-110791825	HepG2	liver:	n/a	n/a
47	MAX	chr3:110790837-110791850	A549	lung:	n/a	n/a
48	TBP	chr3:110789801-110791430	H1-hESC	embryonic stem cell:	n/a	n/a
49	EP300	chr3:110789906-110791623	ECC-1	luminal epithelium:	n/a	chr3:110790548-110790562 chr3:110791039-110791048 chr3:110791076-110791085 chr3:110791039-110791055
50	MAX	chr3:110789106-110791640	HepG2	liver:	n/a	chr3:110789520-110789530

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:110791063-110791113	GM12892	blood:	n/a
2	chr3:110791063-110791113	HNPCEpiC	eye:	n/a
3	chr3:110791063-110791113	SK-N-MC	brain:	n/a
4	chr3:110791063-110791113	GM06990	blood:	n/a
5	chr3:110791063-110791113	IMR90	lung:	fetal
6	chr3:110791063-110791113	RPTEC	kidney:	n/a
7	chr3:110791063-110791113	AG10803	skin:	n/a
8	chr3:110791063-110791113	LNCaP	prostate:	n/a
9	chr3:110791063-110791113	HRE	kidney:	n/a
10	chr3:110791063-110791113	Hepatocyte	liver:	n/a
11	chr3:110791063-110791113	SK-N-SH	brain:	n/a
12	chr3:110791063-110791113	GM19239	blood:	n/a
13	chr3:110791063-110791113	CMK	blood:	n/a
14	chr3:110791063-110791113	PANC-1	pancreas:	n/a
15	chr3:110791063-110791113	MCF10A-Er-Src	breast:	n/a
16	chr3:110791063-110791113	HAEpiC	amniotic membrane:	n/a
17	chr3:110791063-110791113	BJ	skin:	n/a
18	chr3:110791063-110791113	GM12878	blood:	n/a
19	chr3:110791063-110791113	T-47D	breast:	n/a
20	chr3:110791063-110791113	HCF	heart:	n/a
21	chr3:110791063-110791113	SKMC	muscle:	n/a
22	chr3:110791063-110791113	Hela-S3	cervix:	n/a
23	chr3:110791063-110791113	HPAEpiC	pulmonary alveolar:	n/a
24	chr3:110791063-110791113	HMEC	breast:	n/a
25	chr3:110791063-110791113	PFSK-1	brain:	n/a
26	chr3:110791063-110791113	SAEC	small airway:	n/a
27	chr3:110791063-110791113	U87	brain:	n/a
28	chr3:110791063-110791113	HL-60	blood:	n/a
29	chr3:110791063-110791113	HepG2	liver:	n/a
30	chr3:110791063-110791113	AoSMC	blood vessel:	n/a
31	chr3:110791063-110791113	NHBE	bronchial:	n/a
32	chr3:110791063-110791113	ProgFib	skin:	n/a
33	chr3:110791063-110791113	HIPEpiC	eye:	n/a
34	chr3:110791063-110791113	HCT-116	colon:	n/a
35	chr3:110791063-110791113	Caco-2	colon:	n/a
36	chr3:110791063-110791113	MCF-7	breast:	n/a
37	chr3:110791063-110791113	NHDF-neo	bronchial:	n/a
38	chr3:110791063-110791113	HEK293	kidney:	embryo
39	chr3:110791063-110791113	AG04449	skin:	fetal
40	chr3:110791063-110791113	HRPEpiC	eye:	n/a
41	chr3:110791063-110791113	HEEpiC	esophagus:	n/a
42	chr3:110791063-110791113	AG09319	gingival:	n/a
43	chr3:110791063-110791113	HCM	heart:	n/a
44	chr3:110791063-110791113	H1-hESC	embryonic stem cell:	embryo
45	chr3:110791063-110791113	BE2_C	brain:	n/a
46	chr3:110791063-110791113	NB4	blood:	n/a
47	chr3:110791063-110791113	AG04450	lung:	fetal
48	chr3:110791063-110791113	HUVEC	blood vessel:	n/a
49	chr3:110791063-110791113	AG09309	skin:	n/a
50	chr3:110791063-110791113	ovcar-3	ovarian:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr12:68042294..68042958-chr3:110790826..110791329,2	MCF-7	breast:
2	chr12:68041424..68042978-chr3:110790807..110792329,2	MCF-7	breast:
3	chr12:68042169..68042850-chr3:110790806..110791328,5	MCF-7	breast:

No data

Variant related genes	Relation type
PVRL3-AS1	TF binding region
PVRL3	TF binding region
PVRL3	CpG island
PVRL3-AS1	CpG island
ENSG00000127334	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11918904	1.00[AMR][1000 genomes]
rs11921764	1.00[AMR][1000 genomes]
rs11925002	1.00[AMR][1000 genomes]
rs11925004	1.00[AMR][1000 genomes]
rs12489409	1.00[AMR][1000 genomes]
rs1531508	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs16857328	1.00[AMR][1000 genomes]
rs16857332	1.00[AMR][1000 genomes]
rs16857415	1.00[AMR][1000 genomes]
rs16857423	1.00[AMR][1000 genomes]
rs1871024	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs34475462	1.00[AMR][1000 genomes]
rs4682232	1.00[AMR][1000 genomes]
rs59810782	1.00[AMR][1000 genomes]
rs59995070	1.00[AMR][1000 genomes]
rs61178437	1.00[AMR][1000 genomes]
rs6414247	1.00[AMR][1000 genomes]
rs717160	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs723024	1.00[AMR][1000 genomes]
rs72934003	1.00[AMR][1000 genomes]
rs72934016	1.00[AMR][1000 genomes]
rs72934021	1.00[AMR][1000 genomes]
rs72934082	1.00[AMR][1000 genomes]
rs72948764	1.00[AMR][1000 genomes]
rs72948778	1.00[AMR][1000 genomes]
rs72950734	1.00[AMR][1000 genomes]
rs72950741	1.00[AMR][1000 genomes]
rs9824422	1.00[AMR][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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110788400-110791600	Active TSS	Brain Hippocampus Middle	brain
2	chr3:110788400-110792200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:110788400-110792400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:110788400-110793000	Active TSS	Brain Angular Gyrus	brain
5	chr3:110788600-110791600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:110788600-110791600	Active TSS	Brain Cingulate Gyrus	brain
7	chr3:110788600-110792000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:110788600-110792000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:110788600-110792400	Active TSS	Fetal Lung	lung
10	chr3:110788600-110794200	Active TSS	Ovary	ovary
11	chr3:110788600-110794600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr3:110788800-110791800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:110788800-110792200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:110788800-110792400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr3:110788800-110792600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:110788800-110792600	Active TSS	Rectal Smooth Muscle	rectum
17	chr3:110788800-110792600	Active TSS	Right Atrium	heart
18	chr3:110788800-110793200	Active TSS	Fetal Kidney	kidney
19	chr3:110788800-110794000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:110789000-110791400	Active TSS	Placenta	Placenta
21	chr3:110789000-110791800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:110789000-110792000	Active TSS	Brain Anterior Caudate	brain
23	chr3:110789000-110792000	Active TSS	Gastric	stomach
24	chr3:110789000-110792200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:110789000-110792200	Active TSS	Right Ventricle	heart
26	chr3:110789000-110792600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:110789000-110792600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:110789000-110792800	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr3:110789000-110793000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr3:110789000-110793000	Active TSS	Placenta Amnion	Placenta Amnion
31	chr3:110789000-110793200	Active TSS	Fetal Stomach	stomach
32	chr3:110789000-110793200	Active TSS	Stomach Smooth Muscle	stomach
33	chr3:110789000-110793400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:110789000-110793600	Active TSS	NHDF-Ad	bronchial
35	chr3:110789000-110793800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr3:110789000-110794200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:110789200-110791800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr3:110789200-110791800	Active TSS	Brain Substantia Nigra	brain
39	chr3:110789200-110792200	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr3:110789200-110792400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:110789200-110792400	Active TSS	Colon Smooth Muscle	Colon
42	chr3:110789200-110792400	Active TSS	Psoas Muscle	Psoas
43	chr3:110789200-110792600	Active TSS	A549	lung
44	chr3:110789200-110792800	Active TSS	Aorta	Aorta
45	chr3:110789200-110793000	Active TSS	HSMM	muscle
46	chr3:110789200-110793200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:110789200-110793400	Active TSS	Fetal Intestine Large	intestine
48	chr3:110789200-110793600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:110789200-110794200	Active TSS	NHLF	lung
50	chr3:110789200-110794800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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