Variant report

Variant	rs6892588
Chromosome Location	chr5:14676218-14676219
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	EP300	chr5:14675975-14676544	GM12878	blood:	n/a	n/a
2	SPI1	chr5:14676121-14676505	GM12891	blood:	n/a	chr5:14676342-14676355
3	IRF1	chr5:14675744-14676410	K562	blood:	n/a	n/a
4	WRNIP1	chr5:14675645-14677000	GM12878	blood:	n/a	n/a
5	BHLHE40	chr5:14676122-14676473	GM12878	blood:	n/a	n/a
6	PML	chr5:14675463-14677008	GM12878	blood:	n/a	n/a
7	E2F4	chr5:14676098-14676393	GM12878	blood:	n/a	n/a
8	MYC	chr5:14676066-14676918	K562	blood:	n/a	n/a
9	POU2F2	chr5:14675839-14676278	GM12891	blood:	n/a	chr5:14676052-14676065
10	MAX	chr5:14675880-14676963	NB4	blood:	n/a	n/a
11	EBF1	chr5:14676164-14676791	GM12878	blood:	n/a	n/a
12	MYC	chr5:14675975-14677029	K562	blood:	n/a	n/a
13	ZMIZ1	chr5:14676068-14676794	K562	blood:	n/a	n/a
14	JUND	chr5:14676019-14676796	K562	blood:	n/a	chr5:14676729-14676743
15	E2F6	chr5:14676099-14676348	K562	blood:	n/a	chr5:14676236-14676247
16	RUNX3	chr5:14675788-14676887	GM12878	blood:	n/a	chr5:14676648-14676663
17	STAT1	chr5:14676004-14676257	GM12878	blood:	n/a	n/a
18	TAL1	chr5:14675837-14676298	K562	blood:	n/a	n/a
19	RCOR1	chr5:14675946-14676888	K562	blood:	n/a	n/a
20	NFATC1	chr5:14675733-14676774	GM12878	blood:	n/a	n/a
21	MAX	chr5:14676134-14676379	K562	blood:	n/a	n/a
22	NFIC	chr5:14675804-14676595	GM12878	blood:	n/a	n/a
23	MXI1	chr5:14675860-14676667	GM12878	blood:	n/a	n/a
24	NR2F2	chr5:14675875-14676986	K562	blood:	n/a	n/a
25	RUNX3	chr5:14675356-14676865	GM12878	blood:	n/a	chr5:14676648-14676663
26	MAX	chr5:14676065-14676945	K562	blood:	n/a	n/a
27	SPI1	chr5:14676061-14676616	HL-60	blood:	n/a	chr5:14676342-14676355
28	POU2F2	chr5:14675816-14676408	GM12878	blood:	n/a	chr5:14676052-14676065
29	MEF2A	chr5:14675864-14676512	GM12878	blood:	n/a	n/a
30	BCLAF1	chr5:14675804-14676981	GM12878	blood:	n/a	n/a
31	YY1	chr5:14675836-14676314	GM12878	blood:	n/a	n/a
32	SPI1	chr5:14676115-14676496	GM12891	blood:	n/a	chr5:14676342-14676355
33	CHD2	chr5:14676066-14676758	GM12878	blood:	n/a	n/a
34	MAZ	chr5:14676127-14676880	K562	blood:	n/a	n/a
35	STAT5A	chr5:14675577-14676556	GM12878	blood:	n/a	n/a
36	E2F6	chr5:14676034-14676568	H1-hESC	embryonic stem cell:	n/a	chr5:14676236-14676247
37	MTA3	chr5:14675560-14677053	GM12878	blood:	n/a	n/a
38	E2F6	chr5:14676033-14676348	H1-hESC	embryonic stem cell:	n/a	chr5:14676236-14676247
39	FOXM1	chr5:14675660-14676882	GM12878	blood:	n/a	n/a
40	YY1	chr5:14676141-14676436	GM12892	blood:	n/a	n/a
41	TEAD4	chr5:14675507-14676873	K562	blood:	n/a	n/a
42	EP300	chr5:14676052-14676238	SK-N-SH_RA	brain:	n/a	n/a
43	ATF2	chr5:14675748-14676761	GM12878	blood:	n/a	n/a
44	ZNF384	chr5:14675983-14676769	GM12878	blood:	n/a	n/a
45	MYC	chr5:14675921-14676922	NB4	blood:	n/a	n/a
46	SPI1	chr5:14676199-14676424	GM12878	blood:	n/a	chr5:14676342-14676355
47	FOXM1	chr5:14675530-14676756	GM12878	blood:	n/a	n/a
48	E2F6	chr5:14676060-14676397	K562	blood:	n/a	chr5:14676236-14676247
49	ATF2	chr5:14675812-14676457	GM12878	blood:	n/a	n/a
50	E2F6	chr5:14676067-14676919	K562	blood:	n/a	chr5:14676236-14676247

No.	Distal block	Cell Line	Cell type
1	chr5:14675013..14677117-chr5:14685914..14688282,2	MCF-7	breast:
2	chr5:14448785..14450697-chr5:14676194..14678624,2	MCF-7	breast:
3	chr5:14672451..14674258-chr5:14675048..14677621,3	K562	blood:
4	chr5:14673939..14676437-chr5:14678453..14680700,3	K562	blood:
5	chr5:14668622..14671046-chr5:14674810..14676511,2	K562	blood:
6	chr5:14673734..14676543-chr5:14682799..14684871,2	K562	blood:
7	chr5:14674501..14677095-chr5:14686339..14688159,2	K562	blood:
8	chr5:14663431..14670152-chr5:14672054..14680588,17	K562	blood:

Variant related genes	Relation type
FAM105B	TF binding region
ENSG00000154124	Chromatin interaction
ENSG00000261360	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10038397	0.98[EUR][1000 genomes]
rs10052744	1.00[CHD][hapmap]
rs10065032	1.00[EUR][1000 genomes]
rs10078863	0.91[EUR][1000 genomes]
rs10080009	1.00[CHD][hapmap]
rs153921	1.00[CHD][hapmap]
rs153926	1.00[CHD][hapmap]
rs17250963	1.00[CHD][hapmap]
rs17296541	1.00[CHD][hapmap]
rs17363158	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17364066	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[EUR][1000 genomes]
rs187483	1.00[CHD][hapmap]
rs250438	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3045	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs31929	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs3845281	1.00[CHD][hapmap]
rs58936946	0.96[EUR][1000 genomes]
rs59980057	0.93[EUR][1000 genomes]
rs60501770	1.00[EUR][1000 genomes]
rs6884420	1.00[EUR][1000 genomes]
rs6886163	1.00[EUR][1000 genomes]
rs697565	1.00[CHD][hapmap]
rs89356	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs9885040	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv1801565	chr5:14671030-14684471	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6892588	DEDD	trans	parietal	SCAN
rs6892588	FAM105B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14665600-14676600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:14666400-14678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:14666400-14681600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:14666400-14688200	Weak transcription	Ovary	ovary
5	chr5:14666600-14688200	Weak transcription	Brain Germinal Matrix	brain
6	chr5:14667000-14676600	Weak transcription	Fetal Kidney	kidney
7	chr5:14667000-14680000	Weak transcription	Fetal Brain Female	brain
8	chr5:14667000-14681200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:14667000-14690400	Weak transcription	Fetal Brain Male	brain
10	chr5:14667400-14676600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:14668600-14677000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:14668600-14677200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:14669400-14676800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:14669400-14677200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:14671800-14676400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr5:14672000-14684200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:14672200-14676600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:14672200-14690400	Strong transcription	Hela-S3	cervix
19	chr5:14672400-14676400	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:14672600-14678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:14672800-14676400	Weak transcription	Lung	lung
22	chr5:14672800-14676600	Weak transcription	Colonic Mucosa	Colon
23	chr5:14672800-14679200	Weak transcription	HUVEC	blood vessel
24	chr5:14673000-14676400	Weak transcription	Gastric	stomach
25	chr5:14673000-14676400	Weak transcription	Spleen	Spleen
26	chr5:14673000-14678200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:14673000-14679200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:14673000-14679200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:14673000-14681400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:14673200-14676400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:14673200-14676600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:14673200-14681400	Weak transcription	Brain Angular Gyrus	brain
33	chr5:14673600-14676400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:14673800-14677000	Strong transcription	HepG2	liver
35	chr5:14673800-14677200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr5:14673800-14679000	Weak transcription	A549	lung
37	chr5:14673800-14690000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:14674000-14712800	Strong transcription	Fetal Intestine Large	intestine
39	chr5:14674200-14676800	Strong transcription	Fetal Intestine Small	intestine
40	chr5:14674200-14679200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:14674400-14677000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:14674400-14677400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:14674600-14676400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:14674600-14679200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr5:14674600-14681400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr5:14674600-14687200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:14674600-14688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:14674600-14695600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:14674800-14676400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:14674800-14676400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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