Variant report

Variant	rs3892145
Chromosome Location	chr4:6994084-6994085
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	FOS	chr4:6993456-6994213	MCF10A-Er-Src	breast:	n/a	chr4:6993625-6993633 chr4:6993625-6993632
2	ZEB1	chr4:6994000-6994265	GM12878	blood:	n/a	chr4:6994042-6994053
3	MXI1	chr4:6992776-6994296	IMR90	lung:	n/a	n/a
4	POLR2A	chr4:6993748-6994321	K562	blood:	n/a	n/a
5	MYC	chr4:6993454-6994131	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr4:6993488-6994144	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr4:6994070-6994251	K562	blood:	n/a	n/a
8	POLR2A	chr4:6992742-6995081	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr4:6993465-6994104	MCF10A-Er-Src	breast:	n/a	chr4:6993625-6993633 chr4:6993625-6993632
10	FOS	chr4:6993459-6994201	MCF10A-Er-Src	breast:	n/a	chr4:6993625-6993633 chr4:6993625-6993632

No.	Distal block	Cell Line	Cell type
1	chr4:6993091..6995373-chr4:7043423..7046431,3	MCF-7	breast:
2	chr4:6992471..6995105-chr4:7038359..7040025,2	MCF-7	breast:
3	chr4:6988129..6989921-chr4:6992421..6994173,2	K562	blood:

Variant related genes	Relation type
RN7SKP292	TF binding region
TBC1D14	TF binding region
ENSG00000187904	TF binding region
ENSG00000173013	Chromatin interaction
ENSG00000132405	Chromatin interaction
ENSG00000173011	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10009332	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10013211	0.93[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10013696	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10015163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10019256	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10022657	0.96[CEU][hapmap]
rs10022869	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10032908	0.96[CEU][hapmap]
rs10155208	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10804990	0.80[JPT][hapmap]
rs10937762	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap]
rs10937763	0.80[JPT][hapmap]
rs10937771	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12119	0.85[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs12512922	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12648134	0.85[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12650200	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12650264	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13140943	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17742611	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17743234	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301820	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2301821	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28380685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34173965	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35490604	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35772786	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3857168	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3857169	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3857170	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3892976	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4234790	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4315786	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4346651	0.80[JPT][hapmap]
rs4484301	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4608812	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs4689061	0.87[ASN][1000 genomes]
rs4689558	0.85[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs4689571	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4689572	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56307635	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6831368	0.80[JPT][hapmap]
rs6834007	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7672632	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7695050	0.81[ASN][1000 genomes]
rs9291121	0.84[CHD][hapmap]
rs9291123	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs9790586	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs9999127	0.84[AMR][1000 genomes];0.88[EUR][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	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3892145	GRPEL1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6989600-6994400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:6989800-6998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:6990000-6994200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:6990000-6997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:6990200-6994400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr4:6990200-6995200	Enhancers	Brain Substantia Nigra	brain
7	chr4:6990200-6995800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:6990400-6994200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr4:6990400-6994200	Enhancers	Psoas Muscle	Psoas
10	chr4:6990400-6994400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:6990400-6994600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:6990400-7008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:6990600-6994400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr4:6990600-6995600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:6991000-6994200	Genic enhancers	Fetal Muscle Leg	muscle
16	chr4:6991000-6994400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:6991000-6994400	Weak transcription	Fetal Kidney	kidney
18	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:6991200-6995200	Weak transcription	Placenta	Placenta
20	chr4:6991200-6995400	Enhancers	Brain Hippocampus Middle	brain
21	chr4:6991200-6995800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr4:6991200-6996000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr4:6991400-6995400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:6991400-6996000	Weak transcription	Fetal Lung	lung
25	chr4:6991400-7000800	Weak transcription	Colonic Mucosa	Colon
26	chr4:6991600-6994200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:6991600-6994400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:6991600-7000000	Weak transcription	Hela-S3	cervix
29	chr4:6991800-6995200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:6991800-6995800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:6991800-6995800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:6992000-6994400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr4:6992200-6994200	Enhancers	Fetal Heart	heart
34	chr4:6992200-6994600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr4:6992200-6994800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr4:6992200-6995400	Genic enhancers	Fetal Thymus	thymus
37	chr4:6992200-6995600	Enhancers	Primary B cells from cord blood	blood
38	chr4:6992400-6994200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:6992400-6994200	Strong transcription	Fetal Intestine Large	intestine
40	chr4:6992400-6994200	Enhancers	Right Ventricle	heart
41	chr4:6992400-6994400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:6992400-6994600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:6992400-6994600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr4:6992400-6994600	Enhancers	Duodenum Mucosa	Duodenum
45	chr4:6992400-6995000	Genic enhancers	K562	blood
46	chr4:6992400-6995400	Enhancers	Stomach Mucosa	stomach
47	chr4:6992400-6995600	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:6992600-6994400	Enhancers	Fetal Brain Female	brain
49	chr4:6992600-6994400	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr4:6992600-6994600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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