Variant report

Variant	rs13079270
Chromosome Location	chr3:145940962-145940963
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	RAD21	chr3:145940285-145941051	A549	lung:	n/a	n/a
2	RAD21	chr3:145940400-145941038	HCT-116	colon:	n/a	n/a
3	FOSL2	chr3:145940568-145940988	MCF-7	breast:	n/a	n/a
4	RAD21	chr3:145940417-145940993	HepG2	liver:	n/a	n/a
5	RAD21	chr3:145940395-145941033	MCF-7	breast:	n/a	n/a
6	CTCF	chr3:145940598-145940995	MCF-7	breast:	n/a	n/a
7	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
8	TCF12	chr3:145939828-145940981	A549	lung:	n/a	n/a
9	CTCF	chr3:145939765-145941332	A549	lung:	n/a	n/a
10	CTCF	chr3:145940386-145941059	HCT-116	colon:	n/a	n/a
11	RAD21	chr3:145940434-145941063	HCT-116	colon:	n/a	n/a
12	FOS	chr3:145940041-145942138	HUVEC	blood vessel:	n/a	chr3:145941406-145941418 chr3:145941382-145941392 chr3:145941407-145941417 chr3:145941384-145941391 chr3:145941382-145941391 chr3:145941381-145941393 chr3:145941381-145941392 chr3:145941383-145941392 chr3:145941407-145941417 chr3:145941382-145941392
13	RAD21	chr3:145940473-145941044	A549	lung:	n/a	n/a
14	SP1	chr3:145939898-145940995	A549	lung:	n/a	n/a
15	MAX	chr3:145939896-145940967	A549	lung:	n/a	n/a
16	MYBL2	chr3:145939785-145941033	HepG2	liver:	n/a	n/a
17	FOSL2	chr3:145939969-145941586	A549	lung:	n/a	chr3:145941382-145941393 chr3:145941406-145941418 chr3:145941382-145941392 chr3:145941407-145941417 chr3:145941384-145941391 chr3:145941382-145941391 chr3:145941381-145941393 chr3:145941383-145941392 chr3:145941407-145941417 chr3:145941382-145941392
18	EP300	chr3:145939904-145941014	A549	lung:	n/a	n/a
19	SP1	chr3:145939772-145940971	A549	lung:	n/a	n/a
20	ZEB1	chr3:145939969-145941025	HepG2	liver:	n/a	n/a
21	CTCF	chr3:145940427-145941022	MCF-7	breast:	n/a	n/a
22	GATA3	chr3:145939951-145941049	A549	lung:	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: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10460850	0.92[ASN][1000 genomes]
rs10935609	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11926040	0.93[ASN][1000 genomes]
rs12488776	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12629875	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13073184	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs13086396	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13086427	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1398527	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.91[ASN][1000 genomes]
rs1512894	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036979	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175669	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867080	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34773907	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35187466	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35499991	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35616919	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804650	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3828378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828379	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3920230	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61207913	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272407	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808115	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9840954	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13079270	SERP1	cis	cerebellum	SCAN
rs13079270	PLSCR4	cis	parietal	SCAN
rs13079270	PLSCR4	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle
3	chr3:145925000-145945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
6	chr3:145932600-145943800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:145932800-145941000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:145934600-145952200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:145936000-145945200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:145938600-145941200	Active TSS	HepG2	liver
11	chr3:145938600-145941400	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr3:145939800-145941400	Flanking Active TSS	Liver	Liver
13	chr3:145939800-145941400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:145939800-145941400	Flanking Active TSS	A549	lung
15	chr3:145940000-145941000	Enhancers	Ovary	ovary
16	chr3:145940000-145941000	Flanking Active TSS	HUVEC	blood vessel
17	chr3:145940000-145941400	Enhancers	NHLF	lung
18	chr3:145940200-145941200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:145940200-145941200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:145940200-145941400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:145940200-145941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr3:145940200-145941400	Enhancers	Stomach Mucosa	stomach
23	chr3:145940200-145941400	Enhancers	NH-A	brain
24	chr3:145940400-145941000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:145940400-145941000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:145940400-145941000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:145940400-145941000	Enhancers	Left Ventricle	heart
28	chr3:145940400-145941000	Enhancers	Lung	lung
29	chr3:145940400-145941000	Enhancers	Right Atrium	heart
30	chr3:145940400-145941200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:145940400-145941600	Enhancers	Pancreas	Pancrea
32	chr3:145940400-145942000	Enhancers	Fetal Intestine Large	intestine
33	chr3:145940600-145941400	Enhancers	Brain Anterior Caudate	brain
34	chr3:145940600-145941400	Enhancers	Osteobl	bone
35	chr3:145940600-145941600	Enhancers	Gastric	stomach
36	chr3:145940600-145943600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:145940600-145944800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:145940600-145953000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:145940600-145953600	Weak transcription	NHDF-Ad	bronchial
40	chr3:145940800-145941400	Enhancers	Adipose Nuclei	Adipose
41	chr3:145940800-145941400	Enhancers	Duodenum Mucosa	Duodenum
42	chr3:145940800-145941600	Enhancers	Fetal Intestine Small	intestine
43	chr3:145940800-145941600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:145940800-145941800	Weak transcription	Fetal Lung	lung
45	chr3:145940800-145943200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:145940800-145944000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:145940800-145944000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:145940800-145944400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:145940800-145944400	Weak transcription	Fetal Stomach	stomach
50	chr3:145940800-145945000	Weak transcription	Aorta	Aorta

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