Variant report

Variant	rs7623263
Chromosome Location	chr3:145884210-145884211
allele	C/T
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	BCL3	chr3:145883950-145884783	A549	lung:	n/a	n/a
2	GATA3	chr3:145884046-145884639	SK-N-SH	brain:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
3	USF1	chr3:145884164-145884865	A549	lung:	n/a	n/a
4	ATF3	chr3:145884074-145884786	A549	lung:	n/a	n/a
5	TCF7L2	chr3:145884193-145884603	PANC-1	pancreas:	n/a	chr3:145884350-145884360
6	SP1	chr3:145883941-145884976	A549	lung:	n/a	n/a
7	RFX5	chr3:145884089-145884953	Hela-S3	cervix:	n/a	n/a
8	FOS	chr3:145884113-145884794	MCF10A-Er-Src	breast:	n/a	chr3:145884470-145884481
9	SIN3AK20	chr3:145884183-145884638	A549	lung:	n/a	n/a
10	EP300	chr3:145882567-145885019	A549	lung:	n/a	chr3:145884652-145884666 chr3:145884169-145884183 chr3:145883504-145883518 chr3:145883506-145883520
11	NFIC	chr3:145884123-145884614	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr3:145883999-145885146	MCF-7	breast:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
13	CEBPB	chr3:145882861-145885527	Hela-S3	cervix:	n/a	chr3:145884293-145884304 chr3:145885330-145885341 chr3:145885330-145885341 chr3:145885328-145885341
14	JUND	chr3:145883137-145884908	Hela-S3	cervix:	n/a	n/a
15	ATF3	chr3:145884110-145884736	A549	lung:	n/a	n/a
16	TCF7L2	chr3:145884097-145884424	MCF-7	breast:	n/a	chr3:145884350-145884360
17	MAFK	chr3:145884154-145884881	Hela-S3	cervix:	n/a	chr3:145884615-145884626 chr3:145884614-145884628
18	TEAD4	chr3:145884069-145884868	A549	lung:	n/a	n/a
19	SIN3AK20	chr3:145884116-145884748	A549	lung:	n/a	n/a
20	CEBPB	chr3:145884056-145884731	A549	lung:	n/a	chr3:145884293-145884304
21	BCL3	chr3:145884072-145884734	A549	lung:	n/a	n/a
22	BRCA1	chr3:145884019-145884965	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:145884069-145884734	U87	brain:	n/a	n/a
24	FOS	chr3:145884161-145884756	MCF10A-Er-Src	breast:	n/a	chr3:145884470-145884481
25	NR3C1	chr3:145884189-145884591	A549	lung:	n/a	n/a
26	NR3C1	chr3:145884208-145884589	A549	lung:	n/a	n/a
27	CEBPB	chr3:145884160-145884784	A549	lung:	n/a	chr3:145884293-145884304
28	CEBPB	chr3:145883991-145884877	A549	lung:	n/a	chr3:145884293-145884304
29	GABPA	chr3:145884207-145884902	A549	lung:	n/a	n/a
30	GATA2	chr3:145884134-145885044	HUVEC	blood vessel:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
31	POLR2A	chr3:145884132-145884738	MCF10A-Er-Src	breast:	n/a	n/a
32	TCF7L2	chr3:145883974-145884666	Hela-S3	cervix:	n/a	chr3:145884350-145884360
33	SP1	chr3:145884029-145884946	A549	lung:	n/a	n/a
34	FOSL2	chr3:145884119-145884734	A549	lung:	n/a	n/a
35	STAT3	chr3:145884041-145884656	Hela-S3	cervix:	n/a	n/a
36	EP300	chr3:145884102-145885019	Hela-S3	cervix:	n/a	chr3:145884652-145884666 chr3:145884169-145884183
37	RCOR1	chr3:145884089-145884899	Hela-S3	cervix:	n/a	n/a
38	FOS	chr3:145884120-145884919	MCF10A-Er-Src	breast:	n/a	chr3:145884470-145884481
39	TCF12	chr3:145884057-145884972	A549	lung:	n/a	n/a
40	TEAD4	chr3:145884128-145884739	A549	lung:	n/a	n/a
41	MYC	chr3:145883882-145884721	MCF10A-Er-Src	breast:	n/a	n/a
42	STAT3	chr3:145883932-145885084	MCF10A-Er-Src	breast:	n/a	n/a
43	MYC	chr3:145884179-145884612	MCF10A-Er-Src	breast:	n/a	n/a
44	GATA3	chr3:145884046-145884804	A549	lung:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
45	MAX	chr3:145884034-145884931	A549	lung:	n/a	n/a
46	GTF2F1	chr3:145884156-145884741	Hela-S3	cervix:	n/a	n/a
47	GATA3	chr3:145884042-145884697	SK-N-SH	brain:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
48	FOSL2	chr3:145882755-145885023	A549	lung:	n/a	n/a
49	TCF7L2	chr3:145883965-145884939	Hela-S3	cervix:	n/a	chr3:145884350-145884360
50	SMARCC1	chr3:145883678-145884953	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:145883004..145884526-chr3:145908906..145911614,2	MCF-7	breast:
2	chr3:145880474..145882151-chr3:145882740..145884446,2	K562	blood:
3	chr3:145832179..145836696-chr3:145881447..145885871,6	MCF-7	breast:
4	chr3:145736816..145738594-chr3:145881561..145884475,2	MCF-7	breast:

Variant related genes	Relation type
PLOD2	TF binding region
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10935606	0.88[JPT][hapmap]
rs1170389	0.89[JPT][hapmap]
rs1170391	0.89[JPT][hapmap]
rs1170393	0.89[JPT][hapmap]
rs11718741	0.89[JPT][hapmap]
rs13088646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398525	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1707469	0.80[GIH][hapmap];0.89[JPT][hapmap]
rs17414130	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1868541	0.89[JPT][hapmap]
rs1913186	1.00[CEU][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2137485	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2203213	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34800183	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4342076	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4681301	0.89[JPT][hapmap]
rs6766101	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][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	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7623263	CPA3	cis	cerebellum	SCAN
rs7623263	PLOD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145879800-145884400	Weak transcription	Pancreas	Pancrea
2	chr3:145879800-145885000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:145880000-145884400	Weak transcription	Aorta	Aorta
4	chr3:145880000-145884400	Weak transcription	Right Atrium	heart
5	chr3:145880000-145885000	Enhancers	HMEC	breast
6	chr3:145880000-145885000	Enhancers	HSMMtube	muscle
7	chr3:145880000-145885000	Enhancers	NHDF-Ad	bronchial
8	chr3:145880000-145885600	Enhancers	Fetal Intestine Small	intestine
9	chr3:145880200-145884800	Enhancers	HepG2	liver
10	chr3:145880200-145885200	Enhancers	NHLF	lung
11	chr3:145880200-145885600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:145880600-145884400	Weak transcription	Fetal Lung	lung
13	chr3:145880600-145884800	Enhancers	Liver	Liver
14	chr3:145880800-145884400	Weak transcription	Ovary	ovary
15	chr3:145880800-145914400	Weak transcription	Left Ventricle	heart
16	chr3:145881200-145885000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:145881200-145885000	Enhancers	NHEK	skin
18	chr3:145881600-145884800	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:145881600-145885000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:145881600-145885400	Flanking Active TSS	A549	lung
21	chr3:145882000-145884400	Enhancers	Hela-S3	cervix
22	chr3:145882000-145885200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:145882000-145885600	Enhancers	HUVEC	blood vessel
24	chr3:145882200-145885000	Enhancers	Fetal Intestine Large	intestine
25	chr3:145882600-145885200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr3:145882800-145885200	Enhancers	Stomach Mucosa	stomach
27	chr3:145883000-145885000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:145883000-145885200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:145883000-145885400	Enhancers	Colon Smooth Muscle	Colon
30	chr3:145883000-145885400	Enhancers	HSMM	muscle
31	chr3:145883000-145913000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:145883200-145884400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:145883200-145884400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:145883200-145885200	Weak transcription	Fetal Kidney	kidney
35	chr3:145883200-145885400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr3:145883400-145884600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:145883400-145884800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr3:145883400-145885000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:145883600-145884400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:145883600-145885000	Enhancers	Adipose Nuclei	Adipose
41	chr3:145883800-145884600	Enhancers	Stomach Smooth Muscle	stomach
42	chr3:145883800-145884800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr3:145883800-145885000	Enhancers	NH-A	brain
44	chr3:145883800-145890000	Weak transcription	Fetal Heart	heart
45	chr3:145884000-145884400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:145884000-145885400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:145884000-145886200	Enhancers	Osteobl	bone
48	chr3:145884000-145903400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:145884200-145884600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:145884200-145884800	Enhancers	Duodenum Mucosa	Duodenum

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