Variant report

Variant	rs12630390
Chromosome Location	chr3:141030543-141030544
allele	A/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	MAFK	chr3:141030111-141030951	Hela-S3	cervix:	n/a	chr3:141030320-141030335 chr3:141030810-141030825
2	REST	chr3:141030297-141030940	SK-N-SH	brain:	n/a	chr3:141030362-141030375
3	YY1	chr3:141030247-141030834	K562	blood:	n/a	n/a
4	CTCF	chr3:141030535-141031017	GM12878	blood:	n/a	chr3:141030769-141030785 chr3:141030771-141030780
5	POLR2A	chr3:141030262-141031006	GM10847	blood:	n/a	n/a
6	SRF	chr3:141030460-141030866	K562	blood:	n/a	n/a
7	SMC3	chr3:141030408-141031028	K562	blood:	n/a	n/a
8	SP4	chr3:141030431-141030894	H1-hESC	embryonic stem cell:	n/a	chr3:141030697-141030708
9	POLR2A	chr3:141029877-141031261	U87	brain:	n/a	n/a
10	POLR2A	chr3:141029848-141031086	GM18526	blood:	n/a	n/a
11	TEAD4	chr3:141030417-141030926	H1-hESC	embryonic stem cell:	n/a	n/a
12	NFATC1	chr3:141030237-141031220	GM12878	blood:	n/a	chr3:141030663-141030677
13	JUND	chr3:141030409-141030972	A549	lung:	n/a	n/a
14	YY1	chr3:141029886-141030982	GM12892	blood:	n/a	n/a
15	GATA1	chr3:141029608-141033138	K562	blood:	n/a	chr3:141031684-141031693 chr3:141031986-141031996 chr3:141031704-141031714 chr3:141031706-141031723 chr3:141031705-141031714 chr3:141031747-141031755 chr3:141031684-141031691 chr3:141031683-141031693
16	ELF1	chr3:141030357-141030967	HepG2	liver:	n/a	n/a
17	EBF1	chr3:141030363-141031243	GM12878	blood:	n/a	n/a
18	GABPA	chr3:141029843-141031331	MCF-7	breast:	n/a	chr3:141030693-141030700
19	CHD2	chr3:141030372-141030920	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr3:141030398-141031176	K562	blood:	n/a	n/a
21	POLR2A	chr3:141029682-141031738	GM12892	blood:	n/a	n/a
22	YY1	chr3:141030291-141030985	HCT-116	colon:	n/a	n/a
23	YY1	chr3:141030244-141030925	HepG2	liver:	n/a	n/a
24	ATF2	chr3:141030204-141031011	GM12878	blood:	n/a	n/a
25	GATA1	chr3:141030342-141032321	PBDE	blood:	n/a	chr3:141031684-141031693 chr3:141031986-141031996 chr3:141031704-141031714 chr3:141031706-141031723 chr3:141031705-141031714 chr3:141031747-141031755 chr3:141031684-141031691 chr3:141031683-141031693
26	CTCF	chr3:141030485-141031091	K562	blood:	n/a	chr3:141030769-141030785 chr3:141030771-141030780
27	POLR2A	chr3:141030242-141031664	IMR90	lung:	n/a	n/a
28	POLR2A	chr3:141030029-141031068	HCT-116	colon:	n/a	n/a
29	NFIC	chr3:141030217-141030789	HepG2	liver:	n/a	n/a
30	BACH1	chr3:141030341-141030975	H1-hESC	embryonic stem cell:	n/a	n/a
31	ELF1	chr3:141030319-141030972	HepG2	liver:	n/a	n/a
32	SIX5	chr3:141030134-141031282	A549	lung:	n/a	chr3:141030633-141030647 chr3:141030607-141030616 chr3:141030635-141030644 chr3:141030637-141030646
33	MXI1	chr3:141030148-141030995	HepG2	liver:	n/a	n/a
34	NFIC	chr3:141030361-141031036	GM12878	blood:	n/a	n/a
35	E2F4	chr3:141030132-141030915	K562	blood:	n/a	chr3:141030359-141030366
36	POLR2A	chr3:141030294-141031049	GM12891	blood:	n/a	n/a
37	YY1	chr3:141030428-141030867	H1-hESC	embryonic stem cell:	n/a	n/a
38	RUNX3	chr3:141030182-141031355	GM12878	blood:	n/a	n/a
39	ELK4	chr3:141030419-141031026	HEK293	kidney:	n/a	n/a
40	SPI1	chr3:141030449-141030897	HL-60	blood:	n/a	n/a
41	EP300	chr3:141030402-141030955	GM12878	blood:	n/a	n/a
42	SIX5	chr3:141030293-141030858	GM12878	blood:	n/a	chr3:141030633-141030647 chr3:141030607-141030616 chr3:141030635-141030644 chr3:141030637-141030646
43	YY1	chr3:141030384-141030975	K562	blood:	n/a	n/a
44	POLR2A	chr3:141029863-141031123	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:141029448-141031315	PFSK-1	brain:	n/a	n/a
46	SP1	chr3:141030204-141031189	A549	lung:	n/a	chr3:141030697-141030708 chr3:141030317-141030327 chr3:141030323-141030337
47	ZBTB7A	chr3:141030300-141030938	K562	blood:	n/a	n/a
48	CEBPB	chr3:141030381-141030924	Hela-S3	cervix:	n/a	n/a
49	ELF1	chr3:141030051-141031137	MCF-7	breast:	n/a	n/a
50	ELF1	chr3:141029841-141031076	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141030231..141032232-chr3:141071228..141072763,2	K562	blood:
2	chr3:141029221..141032005-chr3:141199464..141200982,2	MCF-7	breast:
3	chr3:141030424..141032274-chr3:141049079..141051494,2	MCF-7	breast:
4	chr3:141030385..141032264-chr3:141049679..141051304,2	K562	blood:
5	chr17:57920552..57922129-chr3:141029319..141031208,2	MCF-7	breast:
6	chr3:141030270..141030782-chr3:141088625..141089300,2	K562	blood:
7	chr3:141020313..141022336-chr3:141030461..141032537,2	MCF-7	breast:
8	chr3:141030275..141032040-chr3:141128069..141130455,2	K562	blood:
9	chr3:141030257..141033623-chr3:141042380..141046909,4	K562	blood:
10	chr13:31040031..31040568-chr3:141030083..141030838,2	HCT-116	colon:
11	chr3:141029860..141032097-chr3:141173989..141175746,3	K562	blood:
12	chr3:141028495..141032567-chr3:141157435..141162053,7	K562	blood:
13	chr3:141030314..141031238-chr3:141279893..141280648,9	K562	blood:
14	chr11:71822694..71823448-chr3:141030148..141030941,2	NB4	blood:
15	chr3:141030082..141030809-chr3:186500629..186501624,2	Hela-S3	cervix:
16	chr3:141030361..141031248-chr3:141079401..141080364,5	MCF-7	breast:
17	chr3:141029007..141031829-chr3:141128539..141131843,4	MCF-7	breast:
18	chr3:140946468..140949037-chr3:141029081..141031629,2	MCF-7	breast:
19	chr3:141030383..141031255-chr3:141170825..141171481,2	MCF-7	breast:
20	chr3:141028766..141032567-chr3:141157435..141160159,4	K562	blood:
21	chr3:141020173..141025458-chr3:141027736..141031856,6	K562	blood:
22	chr3:141030192..141032972-chr3:141205861..141208055,2	K562	blood:
23	chr3:141030343..141031265-chr3:141170565..141171975,8	K562	blood:
24	chr3:141028943..141030664-chr3:141287005..141289345,2	MCF-7	breast:
25	chr3:141023312..141027474-chr3:141027786..141032081,5	MCF-7	breast:
26	chr3:141029632..141032040-chr3:141170273..141172073,2	K562	blood:
27	chr3:141022368..141022878-chr3:141030154..141030708,2	K562	blood:
28	chr3:140998105..140999651-chr3:141029649..141032061,2	K562	blood:
29	chr3:141027145..141033256-chr3:141085204..141089995,12	K562	blood:
30	chr3:141029377..141033531-chr3:141165560..141167342,4	MCF-7	breast:
31	chr3:141011845..141013998-chr3:141030373..141032381,2	MCF-7	breast:
32	chr3:141030231..141032200-chr3:141070469..141074049,3	K562	blood:
33	chr3:141030366..141030894-chr3:141159937..141160843,2	K562	blood:
34	chr3:141028623..141032743-chr3:141076399..141079995,4	K562	blood:
35	chr3:141029410..141031621-chr3:141132926..141134468,2	K562	blood:
36	chr3:141030009..141033814-chr3:141085690..141089850,5	K562	blood:

Variant related genes	Relation type
ENSG00000249540	TF binding region
ENSG00000249540	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction
ENSG00000155893	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000189403	Chromatin interaction
ENSG00000155903	Chromatin interaction
ENSG00000156976	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6773133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955216	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[EUR][1000 genomes]
rs9968231	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr3:141029400-141031000	Active TSS	A549	lung
2	chr3:141029600-141030800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:141029600-141030800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr3:141029600-141031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:141029600-141031000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:141029600-141031000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:141029600-141031000	Active TSS	Rectal Smooth Muscle	rectum
8	chr3:141029600-141031200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:141029600-141031600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr3:141029600-141031600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:141029800-141030600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:141029800-141030800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:141029800-141030800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:141029800-141030800	Active TSS	Fetal Kidney	kidney
15	chr3:141029800-141030800	Active TSS	NHLF	lung
16	chr3:141029800-141031000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:141029800-141031000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:141029800-141031000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:141029800-141031000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:141029800-141031200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:141029800-141031200	Active TSS	Psoas Muscle	Psoas
22	chr3:141029800-141031600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:141029800-141031600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr3:141030000-141030600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:141030000-141030600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:141030000-141030600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:141030000-141030800	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:141030000-141030800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:141030000-141030800	Bivalent/Poised TSS	HepG2	liver
30	chr3:141030000-141030800	Active TSS	HSMM	muscle
31	chr3:141030000-141030800	Active TSS	K562	blood
32	chr3:141030000-141031000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr3:141030000-141031000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr3:141030000-141031000	Active TSS	Small Intestine	intestine
35	chr3:141030000-141031000	Active TSS	GM12878-XiMat	blood
36	chr3:141030000-141031200	Active TSS	Aorta	Aorta
37	chr3:141030000-141031200	Active TSS	Colonic Mucosa	Colon
38	chr3:141030000-141031200	Active TSS	Ovary	ovary
39	chr3:141030000-141031200	Active TSS	Pancreas	Pancrea
40	chr3:141030000-141031400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:141030000-141031400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr3:141030000-141031400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr3:141030200-141030600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:141030200-141030600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr3:141030200-141030800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:141030200-141030800	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:141030200-141030800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:141030200-141030800	Active TSS	Primary B cells from peripheral blood	blood
49	chr3:141030200-141030800	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr3:141030200-141030800	Active TSS	Muscle Satellite Cultured Cells	--

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