Variant report

Variant	rs2036980
Chromosome Location	chr3:145940283-145940284
allele	C/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	ZBTB33	chr3:145940026-145940570	A549	lung:	n/a	n/a
2	HNF4A	chr3:145940019-145940466	HepG2	liver:	n/a	chr3:145940264-145940279
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	POLR2A	chr3:145939975-145940579	HepG2	liver:	n/a	n/a
8	MAFK	chr3:145940113-145940398	HepG2	liver:	n/a	n/a
9	ELF1	chr3:145940035-145940498	HepG2	liver:	n/a	n/a
10	CEBPB	chr3:145940113-145940674	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:145940001-145940824	HepG2	liver:	n/a	n/a
12	HDAC2	chr3:145939941-145940512	HepG2	liver:	n/a	n/a
13	HNF4A	chr3:145940002-145940811	HepG2	liver:	n/a	chr3:145940264-145940279
14	HEY1	chr3:145939958-145940653	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:145940007-145940875	HUVEC	blood vessel:	n/a	n/a
16	FOXA2	chr3:145939465-145940841	HepG2	liver:	n/a	n/a
17	ARID3A	chr3:145939594-145940831	HepG2	liver:	n/a	n/a
18	SP1	chr3:145939943-145940859	HepG2	liver:	n/a	n/a
19	FOXA2	chr3:145939934-145940854	A549	lung:	n/a	n/a
20	JUN	chr3:145940136-145940880	HepG2	liver:	n/a	n/a
21	MAFF	chr3:145940099-145940818	HepG2	liver:	n/a	n/a
22	MBD4	chr3:145940052-145940808	HepG2	liver:	n/a	n/a
23	EP300	chr3:145939909-145940605	A549	lung:	n/a	n/a
24	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
25	TCF12	chr3:145939828-145940981	A549	lung:	n/a	n/a
26	CTCF	chr3:145939765-145941332	A549	lung:	n/a	n/a
27	MAFK	chr3:145940016-145940802	HepG2	liver:	n/a	n/a
28	ELF1	chr3:145940042-145940525	HepG2	liver:	n/a	n/a
29	USF1	chr3:145940001-145940848	A549	lung:	n/a	n/a
30	MAX	chr3:145940251-145940695	HepG2	liver:	n/a	n/a
31	NFIC	chr3:145939555-145940880	HepG2	liver:	n/a	n/a
32	FOXA1	chr3:145939874-145940509	HepG2	liver:	n/a	n/a
33	REST	chr3:145939895-145940893	A549	lung:	n/a	n/a
34	NR2F2	chr3:145940021-145940664	HepG2	liver:	n/a	n/a
35	HEY1	chr3:145939889-145940841	HepG2	liver:	n/a	n/a
36	EP300	chr3:145939872-145940949	HepG2	liver:	n/a	n/a
37	CEBPZ	chr3:145940149-145940488	HepG2	liver:	n/a	n/a
38	MXI1	chr3:145940006-145940804	HepG2	liver:	n/a	n/a
39	MBD4	chr3:145939806-145940898	HepG2	liver:	n/a	n/a
40	CTCF	chr3:145940160-145940310	A549	lung:	n/a	n/a
41	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
42	RAD21	chr3:145940273-145940910	A549	lung:	n/a	n/a
43	REST	chr3:145939999-145940764	HepG2	liver:	n/a	n/a
44	EP300	chr3:145940084-145940447	HepG2	liver:	n/a	n/a
45	NFIC	chr3:145940054-145940852	HepG2	liver:	n/a	n/a
46	FOSL2	chr3:145940092-145940952	HepG2	liver:	n/a	n/a
47	TBP	chr3:145940018-145940728	HepG2	liver:	n/a	n/a
48	RAD21	chr3:145940103-145940919	HepG2	liver:	n/a	n/a
49	BHLHE40	chr3:145940155-145940799	HepG2	liver:	n/a	n/a
50	POLR2A	chr3:145939896-145940711	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145940254..145941134-chr3:146295120..146295978,3	MCF-7	breast:

Variant related genes	Relation type
PLSCR4	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10737947	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs10804709	0.80[ASN][1000 genomes]
rs10804710	0.93[ASN][1000 genomes]
rs10935611	0.94[CHB][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10935613	0.93[ASN][1000 genomes]
rs10935614	0.93[ASN][1000 genomes]
rs10935615	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10935616	0.93[ASN][1000 genomes]
rs11709096	0.93[ASN][1000 genomes]
rs11716310	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915448	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs11919011	0.93[ASN][1000 genomes]
rs12487353	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12633074	0.93[ASN][1000 genomes]
rs1398125	0.82[ASN][1000 genomes]
rs1398529	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512078	0.93[ASN][1000 genomes]
rs1512079	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1512080	0.84[ASN][1000 genomes]
rs1512081	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs1512888	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512890	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1512893	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1606434	0.84[ASN][1000 genomes]
rs1877511	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1913184	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175544	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs2175545	0.93[ASN][1000 genomes]
rs2867081	0.93[ASN][1000 genomes]
rs2867082	0.84[ASN][1000 genomes]
rs2867083	0.93[ASN][1000 genomes]
rs2867084	0.92[ASN][1000 genomes]
rs2903478	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903479	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3762686	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804648	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3914252	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273339	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.93[ASN][1000 genomes]
rs4475004	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4488802	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs4681306	0.93[ASN][1000 genomes]
rs4681307	0.93[ASN][1000 genomes]
rs4681308	0.93[ASN][1000 genomes]
rs6440421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440422	0.93[ASN][1000 genomes]
rs6770057	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs6770163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775520	0.82[ASN][1000 genomes]
rs6792732	0.93[ASN][1000 genomes]
rs6800307	0.82[ASN][1000 genomes]
rs6805377	0.93[ASN][1000 genomes]
rs7430290	0.93[ASN][1000 genomes]
rs7612683	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621841	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs7632412	0.93[ASN][1000 genomes]
rs7633252	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7634568	0.93[ASN][1000 genomes]
rs7643778	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs9756128	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809892	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813122	0.93[ASN][1000 genomes]
rs9822280	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825776	0.93[ASN][1000 genomes]
rs9826132	0.93[ASN][1000 genomes]
rs9826360	0.93[ASN][1000 genomes]
rs9826591	0.84[ASN][1000 genomes]
rs9830892	0.84[ASN][1000 genomes]
rs9836419	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs9838801	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838866	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs9839724	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839874	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845890	0.93[ASN][1000 genomes]
rs9850566	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851511	0.93[ASN][1000 genomes]
rs9855695	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs9858823	0.84[ASN][1000 genomes]
rs9859273	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs9863647	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.93[ASN][1000 genomes]
rs9867851	0.93[ASN][1000 genomes]
rs9873891	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9875799	0.93[ASN][1000 genomes]
rs9877004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2036980	GPR87	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145914800-145940400	Weak transcription	Spleen	Spleen
2	chr3:145917800-145940400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:145918000-145940400	Weak transcription	Pancreas	Pancrea
4	chr3:145918400-145940400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:145920600-145940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:145922600-145940400	Weak transcription	Lung	lung
7	chr3:145924400-145944000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:145924400-145945200	Weak transcription	HSMMtube	muscle
9	chr3:145925000-145945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:145925400-145952800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:145925600-145950800	Weak transcription	Fetal Kidney	kidney
12	chr3:145932600-145943800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:145932800-145941000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:145934000-145940400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:145934600-145952200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:145935200-145940400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:145935200-145940400	Weak transcription	Left Ventricle	heart
18	chr3:145935600-145940400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:145936000-145945200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:145936200-145940400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:145938200-145940400	Enhancers	Adipose Nuclei	Adipose
22	chr3:145938600-145940400	Enhancers	Fetal Intestine Small	intestine
23	chr3:145938600-145941200	Active TSS	HepG2	liver
24	chr3:145938600-145941400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:145938800-145940600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:145938800-145940800	Enhancers	Fetal Lung	lung
27	chr3:145939000-145940600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:145939200-145940600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:145939200-145940600	Enhancers	NHDF-Ad	bronchial
30	chr3:145939200-145940800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:145939200-145940800	Enhancers	Stomach Smooth Muscle	stomach
32	chr3:145939200-145940800	Enhancers	Hela-S3	cervix
33	chr3:145939400-145940400	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:145939400-145940400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:145939400-145940400	Weak transcription	Right Atrium	heart
36	chr3:145939600-145940600	Weak transcription	Brain Anterior Caudate	brain
37	chr3:145939800-145940400	Weak transcription	Small Intestine	intestine
38	chr3:145939800-145940800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:145939800-145941400	Flanking Active TSS	Liver	Liver
40	chr3:145939800-145941400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:145939800-145941400	Flanking Active TSS	A549	lung
42	chr3:145940000-145940400	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr3:145940000-145940600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:145940000-145940600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:145940000-145940600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:145940000-145940800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr3:145940000-145941000	Enhancers	Ovary	ovary
48	chr3:145940000-145941000	Flanking Active TSS	HUVEC	blood vessel
49	chr3:145940000-145941400	Enhancers	NHLF	lung
50	chr3:145940200-145940400	Enhancers	Colonic Mucosa	Colon

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