Variant report

Variant	rs4142872
Chromosome Location	chr2:231280632-231280633
allele	G/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	POLR2A	chr2:231280615-231281133	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:231280600-231281449	IMR90	lung:	n/a	n/a
3	POLR2A	chr2:231280589-231281202	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr2:231280506-231281396	K562	blood:	n/a	n/a
5	SPI1	chr2:231280585-231281125	GM12891	blood:	n/a	n/a
6	PML	chr2:231280528-231281669	GM12878	blood:	n/a	n/a
7	POU2F2	chr2:231280609-231281211	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:231280589-231281277	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr2:231280434-231281333	GM12878	blood:	n/a	n/a
10	FOXM1	chr2:231280556-231281546	GM12878	blood:	n/a	n/a
11	ELF1	chr2:231280626-231281147	HepG2	liver:	n/a	chr2:231280907-231280920
12	NFIC	chr2:231280398-231281493	GM12878	blood:	n/a	n/a
13	NFATC1	chr2:231280607-231281188	GM12878	blood:	n/a	n/a
14	YY1	chr2:231280606-231281104	HepG2	liver:	n/a	n/a
15	POU2F2	chr2:231280610-231281151	GM12891	blood:	n/a	n/a
16	SPI1	chr2:231280249-231281369	GM12878	blood:	n/a	chr2:231280539-231280552
17	POLR2A	chr2:231280515-231281314	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:231280444-231281389	HUVEC	blood vessel:	n/a	n/a
19	MEF2A	chr2:231280606-231281391	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:231280595-231281279	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr2:231280625-231281171	K562	blood:	n/a	n/a
22	IRF1	chr2:231280514-231281564	K562	blood:	n/a	chr2:231280851-231280861 chr2:231280845-231280866 chr2:231280851-231280865 chr2:231280845-231280862 chr2:231280850-231280862 chr2:231280849-231280860
23	POLR2A	chr2:231280539-231281246	Hela-S3	cervix:	n/a	n/a
24	PRDM1	chr2:231280629-231281059	Hela-S3	cervix:	n/a	chr2:231280847-231280862 chr2:231280849-231280858 chr2:231280848-231280862 chr2:231280849-231280862
25	CEBPB	chr2:231280494-231281444	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr2:231280440-231281344	U87	brain:	n/a	n/a
27	ELF1	chr2:231280614-231281161	A549	lung:	n/a	chr2:231280907-231280920
28	POLR2A	chr2:231280216-231281274	GM12891	blood:	n/a	n/a
29	MXI1	chr2:231280272-231281937	IMR90	lung:	n/a	n/a
30	ELF1	chr2:231280632-231281194	SK-N-SH	brain:	n/a	chr2:231280907-231280920
31	POLR2A	chr2:231280532-231281264	PFSK-1	brain:	n/a	n/a
32	HCFC1	chr2:231280357-231281753	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:231280192-231281486	GM12892	blood:	n/a	n/a
34	IRF4	chr2:231280562-231281128	GM12878	blood:	n/a	chr2:231280845-231280866
35	SP1	chr2:231280614-231281089	GM12878	blood:	n/a	n/a
36	FOSL2	chr2:231280596-231281239	SK-N-SH	brain:	n/a	chr2:231280888-231280898 chr2:231280888-231280898 chr2:231280888-231280898
37	POLR2A	chr2:231280601-231281131	HL-60	blood:	n/a	n/a
38	POLR2A	chr2:231280406-231281652	Hela-S3	cervix:	n/a	n/a
39	RUNX3	chr2:231280532-231281172	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:231279849-231281725	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:231280390-231281541	GM19099	blood:	n/a	n/a
42	POLR2A	chr2:231280480-231281713	GM12891	blood:	n/a	n/a
43	ELF1	chr2:231280626-231281466	HCT-116	colon:	n/a	chr2:231280907-231280920
44	POLR2A	chr2:231280611-231281366	HepG2	liver:	n/a	n/a
45	CEBPB	chr2:231280562-231281475	GM12878	blood:	n/a	n/a
46	NFIC	chr2:231280505-231281393	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:231280235-231281170	GM12878	blood:	n/a	n/a
48	ATF2	chr2:231280632-231281470	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:231280625-231281194	Hela-S3	cervix:	n/a	n/a
50	TEAD4	chr2:231280516-231281387	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:231191663..231192385-chr2:231280228..231281288,3	Hela-S3	cervix:
2	chr2:231191400..231192273-chr2:231280039..231281003,2	MCF-7	breast:
3	chr2:231191754..231192275-chr2:231280477..231281313,4	HCT-116	colon:
4	chr2:231280254..231281169-chr8:125462695..125463364,2	NB4	blood:
5	chr12:6981832..6982808-chr2:231280454..231281321,2	Hela-S3	cervix:

Variant related genes	Relation type
SP100	TF binding region
ENSG00000111671	Chromatin interaction
ENSG00000185404	Chromatin interaction
ENSG00000010626	Chromatin interaction
ENSG00000240370	Chromatin interaction
ENSG00000183665	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10180055	0.88[ASN][1000 genomes]
rs10180131	0.90[ASN][1000 genomes]
rs10191049	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10207311	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10804365	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11682084	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11688912	0.86[ASN][1000 genomes]
rs11689240	0.90[ASN][1000 genomes]
rs11690286	0.90[ASN][1000 genomes]
rs11898168	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13411346	0.88[ASN][1000 genomes]
rs13411566	0.92[ASN][1000 genomes]
rs3754944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs56102622	0.88[ASN][1000 genomes]
rs56377716	0.87[ASN][1000 genomes]
rs62193378	0.88[ASN][1000 genomes]
rs62193388	0.88[ASN][1000 genomes]
rs6436937	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6722012	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6730329	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6748062	0.92[ASN][1000 genomes]
rs6748069	0.92[ASN][1000 genomes]
rs6756448	0.91[ASN][1000 genomes]
rs7581828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7582700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7595408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs973504	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4142872	LOC93349	cis	multi-tissue	Pritchard
rs4142872	NMUR1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231277200-231280800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:231279200-231281000	Enhancers	Spleen	Spleen
3	chr2:231279800-231280800	Flanking Active TSS	Dnd41	blood
4	chr2:231280000-231280800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:231280000-231283600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr2:231280200-231280800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:231280200-231280800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr2:231280200-231280800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr2:231280200-231280800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:231280200-231281400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr2:231280400-231280800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:231280400-231280800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:231280400-231280800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:231280400-231280800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr2:231280400-231280800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr2:231280400-231280800	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr2:231280400-231280800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr2:231280400-231280800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:231280400-231280800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr2:231280400-231280800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr2:231280400-231280800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:231280400-231280800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr2:231280400-231280800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:231280400-231280800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:231280400-231280800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:231280400-231280800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr2:231280400-231280800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr2:231280400-231280800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:231280400-231280800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:231280400-231280800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:231280400-231280800	Flanking Active TSS	Aorta	Aorta
32	chr2:231280400-231280800	Flanking Active TSS	Liver	Liver
33	chr2:231280400-231280800	Flanking Active TSS	Colonic Mucosa	Colon
34	chr2:231280400-231280800	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr2:231280400-231280800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr2:231280400-231280800	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr2:231280400-231280800	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr2:231280400-231280800	Flanking Active TSS	Fetal Thymus	thymus
39	chr2:231280400-231280800	Flanking Active TSS	Left Ventricle	heart
40	chr2:231280400-231280800	Flanking Active TSS	Psoas Muscle	Psoas
41	chr2:231280400-231280800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr2:231280400-231280800	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr2:231280400-231280800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr2:231280400-231280800	Flanking Active TSS	Stomach Mucosa	stomach
45	chr2:231280400-231280800	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr2:231280400-231280800	Flanking Active TSS	Thymus	Thymus
47	chr2:231280400-231280800	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:231280400-231280800	Flanking Active TSS	Hela-S3	cervix
49	chr2:231280400-231280800	Flanking Active TSS	HepG2	liver
50	chr2:231280400-231280800	Flanking Active TSS	HMEC	breast

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