Variant report

Variant	rs9880432
Chromosome Location	chr3:145940573-145940574
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	RAD21	chr3:145940285-145941051	A549	lung:	n/a	n/a
2	CTCF	chr3:145940569-145940804	MCF-7	breast:	n/a	n/a
3	BCL3	chr3:145939979-145940826	A549	lung:	n/a	n/a
4	MYBL2	chr3:145939969-145940940	HepG2	liver:	n/a	n/a
5	FOXA1	chr3:145939821-145940939	HepG2	liver:	n/a	n/a
6	NR2F2	chr3:145940021-145940950	MCF-7	breast:	n/a	n/a
7	RAD21	chr3:145940400-145941038	HCT-116	colon:	n/a	n/a
8	POLR2A	chr3:145939975-145940579	HepG2	liver:	n/a	n/a
9	RAD21	chr3:145940502-145940944	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPB	chr3:145940113-145940674	HepG2	liver:	n/a	n/a
11	CTCF	chr3:145940511-145940797	K562	blood:	n/a	n/a
12	FOSL2	chr3:145940568-145940988	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:145940001-145940824	HepG2	liver:	n/a	n/a
14	HNF4A	chr3:145940002-145940811	HepG2	liver:	n/a	chr3:145940264-145940279
15	HEY1	chr3:145939958-145940653	HepG2	liver:	n/a	n/a
16	FOSL2	chr3:145940535-145940897	A549	lung:	n/a	n/a
17	POLR2A	chr3:145940007-145940875	HUVEC	blood vessel:	n/a	n/a
18	RAD21	chr3:145940417-145940993	HepG2	liver:	n/a	n/a
19	FOXA2	chr3:145939465-145940841	HepG2	liver:	n/a	n/a
20	ARID3A	chr3:145939594-145940831	HepG2	liver:	n/a	n/a
21	CTCF	chr3:145940566-145940817	MCF-7	breast:	n/a	n/a
22	RAD21	chr3:145940395-145941033	MCF-7	breast:	n/a	n/a
23	SP1	chr3:145939943-145940859	HepG2	liver:	n/a	n/a
24	FOXA2	chr3:145939934-145940854	A549	lung:	n/a	n/a
25	JUN	chr3:145940136-145940880	HepG2	liver:	n/a	n/a
26	MYC	chr3:145940571-145940702	MCF-7	breast:	n/a	n/a
27	POLR2A	chr3:145940292-145940718	HepG2	liver:	n/a	n/a
28	MAFF	chr3:145940099-145940818	HepG2	liver:	n/a	n/a
29	MBD4	chr3:145940052-145940808	HepG2	liver:	n/a	n/a
30	EP300	chr3:145939909-145940605	A549	lung:	n/a	n/a
31	JUND	chr3:145940043-145941577	HepG2	liver:	n/a	chr3:145941406-145941418 chr3:145941381-145941392 chr3:145941382-145941392 chr3:145941407-145941417 chr3:145941384-145941391 chr3:145941382-145941391 chr3:145941381-145941393 chr3:145941383-145941392 chr3:145941407-145941417 chr3:145941382-145941392
32	TCF12	chr3:145939828-145940981	A549	lung:	n/a	n/a
33	CTCF	chr3:145939765-145941332	A549	lung:	n/a	n/a
34	MAFK	chr3:145940016-145940802	HepG2	liver:	n/a	n/a
35	CTCF	chr3:145940446-145940851	H1-hESC	embryonic stem cell:	n/a	n/a
36	USF1	chr3:145940001-145940848	A549	lung:	n/a	n/a
37	MAX	chr3:145940251-145940695	HepG2	liver:	n/a	n/a
38	NFIC	chr3:145939555-145940880	HepG2	liver:	n/a	n/a
39	REST	chr3:145939895-145940893	A549	lung:	n/a	n/a
40	NR2F2	chr3:145940021-145940664	HepG2	liver:	n/a	n/a
41	JUND	chr3:145940552-145940928	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:145940555-145940847	MCF-7	breast:	n/a	n/a
43	CTCF	chr3:145940386-145941059	HCT-116	colon:	n/a	n/a
44	CTCF	chr3:145940543-145940834	H1-hESC	embryonic stem cell:	n/a	n/a
45	HEY1	chr3:145939889-145940841	HepG2	liver:	n/a	n/a
46	EP300	chr3:145939872-145940949	HepG2	liver:	n/a	n/a
47	JUND	chr3:145940503-145940887	A549	lung:	n/a	n/a
48	MXI1	chr3:145940006-145940804	HepG2	liver:	n/a	n/a
49	RAD21	chr3:145940434-145941063	HCT-116	colon:	n/a	n/a
50	MBD4	chr3:145939806-145940898	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145940299..145941372-chr3:146044662..146045624,8	MCF-7	breast:
2	chr3:145940254..145941134-chr3:146295120..146295978,3	MCF-7	breast:

Variant related genes	Relation type
PLSCR4	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1061409	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13326891	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398526	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398528	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1398530	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418885	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762685	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762687	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804647	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804649	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4314144	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57294001	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57764107	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59965250	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766725	0.86[AFR][1000 genomes]
rs6792036	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792166	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792604	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804987	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72991486	0.86[AFR][1000 genomes]
rs72991490	0.86[AFR][1000 genomes]
rs72991494	0.86[AFR][1000 genomes]
rs7611293	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611299	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7611459	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611582	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633567	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809574	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814972	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821768	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830885	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838816	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840954	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844172	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849036	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850144	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854377	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854697	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870547	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870686	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870699	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874072	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874112	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874234	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876826	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9876833	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145920600-145940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle
4	chr3:145925000-145945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
7	chr3:145932600-145943800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:145932800-145941000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:145934600-145952200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:145936000-145945200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:145938600-145941200	Active TSS	HepG2	liver
12	chr3:145938600-145941400	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr3:145938800-145940600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:145938800-145940800	Enhancers	Fetal Lung	lung
15	chr3:145939000-145940600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:145939200-145940600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:145939200-145940600	Enhancers	NHDF-Ad	bronchial
18	chr3:145939200-145940800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:145939200-145940800	Enhancers	Stomach Smooth Muscle	stomach
20	chr3:145939200-145940800	Enhancers	Hela-S3	cervix
21	chr3:145939600-145940600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:145939800-145940800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:145939800-145941400	Flanking Active TSS	Liver	Liver
24	chr3:145939800-145941400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr3:145939800-145941400	Flanking Active TSS	A549	lung
26	chr3:145940000-145940600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:145940000-145940600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:145940000-145940600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:145940000-145940800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:145940000-145941000	Enhancers	Ovary	ovary
31	chr3:145940000-145941000	Flanking Active TSS	HUVEC	blood vessel
32	chr3:145940000-145941400	Enhancers	NHLF	lung
33	chr3:145940200-145940600	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:145940200-145940600	Flanking Active TSS	Osteobl	bone
35	chr3:145940200-145940800	Enhancers	H9 Cell Line	embryonic stem cell
36	chr3:145940200-145940800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:145940200-145940800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:145940200-145940800	Enhancers	Aorta	Aorta
39	chr3:145940200-145940800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:145940200-145940800	Enhancers	Fetal Stomach	stomach
41	chr3:145940200-145940800	Enhancers	Psoas Muscle	Psoas
42	chr3:145940200-145941200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:145940200-145941200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:145940200-145941400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr3:145940200-145941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr3:145940200-145941400	Enhancers	Stomach Mucosa	stomach
47	chr3:145940200-145941400	Enhancers	NH-A	brain
48	chr3:145940400-145940600	Flanking Active TSS	Gastric	stomach
49	chr3:145940400-145940600	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr3:145940400-145940800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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