Variant report

Variant	rs3759579
Chromosome Location	chr14:103851272-103851273
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	YY1	chr14:103851155-103852740	GM12892	blood:	n/a	chr14:103851518-103851532 chr14:103851787-103851798 chr14:103851742-103851750 chr14:103851787-103851801 chr14:103851774-103851788 chr14:103851744-103851752 chr14:103851741-103851751 chr14:103852097-103852106 chr14:103851741-103851763 chr14:103851961-103851975 chr14:103851783-103851797 chr14:103851739-103851758 chr14:103851740-103851752
2	TAF1	chr14:103851165-103851873	SK-N-SH	brain:	n/a	n/a
3	TAF1	chr14:103851258-103852233	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr14:103851181-103851947	A549	lung:	n/a	chr14:103851790-103851806 chr14:103851711-103851727 chr14:103851704-103851711 chr14:103851782-103851791 chr14:103851888-103851904 chr14:103851787-103851803
5	GABPA	chr14:103851228-103852171	SK-N-SH	brain:	n/a	chr14:103852100-103852109
6	YY1	chr14:103851173-103852230	SK-N-SH	brain:	n/a	chr14:103851518-103851532 chr14:103851787-103851798 chr14:103851742-103851750 chr14:103851787-103851801 chr14:103851774-103851788 chr14:103851744-103851752 chr14:103851741-103851751 chr14:103852097-103852106 chr14:103851741-103851763 chr14:103851961-103851975 chr14:103851783-103851797 chr14:103851739-103851758 chr14:103851740-103851752
7	MTA3	chr14:103851194-103852382	GM12878	blood:	n/a	n/a
8	EP300	chr14:103851209-103852098	MCF-7	breast:	n/a	chr14:103851790-103851806 chr14:103851963-103851972 chr14:103851711-103851727 chr14:103851704-103851711 chr14:103851961-103851970 chr14:103851782-103851791 chr14:103851888-103851904 chr14:103851967-103851976 chr14:103851787-103851803
9	POLR2A	chr14:103851237-103851928	SK-N-SH	brain:	n/a	n/a
10	MAFK	chr14:103851222-103851868	IMR90	lung:	n/a	chr14:103851812-103851826 chr14:103851455-103851469
11	GABPA	chr14:103851009-103852225	MCF-7	breast:	n/a	chr14:103852100-103852109
12	POLR2A	chr14:103851226-103852149	HepG2	liver:	n/a	n/a
13	GABPA	chr14:103851197-103852342	A549	lung:	n/a	chr14:103852100-103852109
14	GABPA	chr14:103850724-103852320	MCF-7	breast:	n/a	chr14:103852100-103852109
15	YY1	chr14:103851261-103852007	GM12891	blood:	n/a	chr14:103851518-103851532 chr14:103851787-103851798 chr14:103851742-103851750 chr14:103851787-103851801 chr14:103851774-103851788 chr14:103851744-103851752 chr14:103851741-103851751 chr14:103851741-103851763 chr14:103851961-103851975 chr14:103851783-103851797 chr14:103851739-103851758 chr14:103851740-103851752
16	RCOR1	chr14:103851264-103852118	K562	blood:	n/a	n/a
17	GABPA	chr14:103851154-103852155	SK-N-SH	brain:	n/a	chr14:103852100-103852109
18	EP300	chr14:103851187-103851790	A549	lung:	n/a	chr14:103851711-103851727 chr14:103851704-103851711
19	RFX5	chr14:103851213-103853101	Hela-S3	cervix:	n/a	chr14:103851627-103851642 chr14:103852700-103852713 chr14:103851628-103851642 chr14:103851630-103851639
20	HDAC2	chr14:103850895-103852203	MCF-7	breast:	n/a	n/a
21	SIN3A	chr14:103850997-103853175	H1-hESC	embryonic stem cell:	n/a	chr14:103851219-103851230 chr14:103852202-103852215 chr14:103851800-103851811
22	TCF12	chr14:103851179-103852190	ECC-1	luminal epithelium:	n/a	chr14:103851200-103851210
23	POLR2A	chr14:103850814-103852207	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr14:103851107-103852093	PFSK-1	brain:	n/a	n/a
25	EGR1	chr14:103851267-103852045	ECC-1	luminal epithelium:	n/a	chr14:103851597-103851610 chr14:103851598-103851608 chr14:103851854-103851863 chr14:103851598-103851607 chr14:103851597-103851610 chr14:103851597-103851610 chr14:103851596-103851610 chr14:103851597-103851610 chr14:103851703-103851712
26	MAX	chr14:103851253-103852217	A549	lung:	n/a	n/a
27	SP1	chr14:103851254-103851987	A549	lung:	n/a	n/a
28	FOS	chr14:103851240-103851787	HUVEC	blood vessel:	n/a	chr14:103851668-103851677
29	PML	chr14:103851214-103853112	GM12878	blood:	n/a	n/a
30	RAD21	chr14:103851214-103852278	IMR90	lung:	n/a	chr14:103851708-103851722 chr14:103851223-103851236 chr14:103851791-103851804 chr14:103851546-103851559
31	EGR1	chr14:103851126-103851919	MCF-7	breast:	n/a	chr14:103851597-103851610 chr14:103851598-103851608 chr14:103851854-103851863 chr14:103851598-103851607 chr14:103851597-103851610 chr14:103851597-103851610 chr14:103851596-103851610 chr14:103851597-103851610 chr14:103851703-103851712
32	YY1	chr14:103851258-103852308	HepG2	liver:	n/a	chr14:103851518-103851532 chr14:103851787-103851798 chr14:103851742-103851750 chr14:103851787-103851801 chr14:103851774-103851788 chr14:103851744-103851752 chr14:103851741-103851751 chr14:103852097-103852106 chr14:103851741-103851763 chr14:103851961-103851975 chr14:103851783-103851797 chr14:103851739-103851758 chr14:103851740-103851752
33	E2F6	chr14:103851244-103851995	A549	lung:	n/a	chr14:103851784-103851794 chr14:103851670-103851679 chr14:103851854-103851863 chr14:103851781-103851791
34	EP300	chr14:103851251-103851821	SK-N-SH_RA	brain:	n/a	chr14:103851790-103851806 chr14:103851711-103851727 chr14:103851704-103851711 chr14:103851782-103851791 chr14:103851787-103851803
35	ZBTB7A	chr14:103851107-103851833	ECC-1	luminal epithelium:	n/a	n/a
36	MXI1	chr14:103850656-103853805	SK-N-SH	brain:	n/a	n/a
37	MAX	chr14:103851210-103852129	SK-N-SH	brain:	n/a	n/a
38	MAX	chr14:103851224-103851983	SK-N-SH	brain:	n/a	n/a
39	EGR1	chr14:103850944-103852163	HCT-116	colon:	n/a	chr14:103851597-103851610 chr14:103851598-103851608 chr14:103851078-103851091 chr14:103851854-103851863 chr14:103851598-103851607 chr14:103851597-103851610 chr14:103851597-103851610 chr14:103851596-103851610 chr14:103851597-103851610 chr14:103851703-103851712
40	CEBPB	chr14:103850988-103851997	MCF-7	breast:	n/a	n/a
41	RFX5	chr14:103850987-103852803	IMR90	lung:	n/a	chr14:103851627-103851642 chr14:103852700-103852713 chr14:103851628-103851642 chr14:103851630-103851639
42	YY1	chr14:103851200-103852086	SK-N-SH_RA	brain:	n/a	chr14:103851518-103851532 chr14:103851787-103851798 chr14:103851742-103851750 chr14:103851787-103851801 chr14:103851774-103851788 chr14:103851744-103851752 chr14:103851741-103851751 chr14:103851741-103851763 chr14:103851961-103851975 chr14:103851783-103851797 chr14:103851739-103851758 chr14:103851740-103851752
43	GABPA	chr14:103851111-103852198	HL-60	blood:	n/a	chr14:103852100-103852109
44	JUND	chr14:103851143-103852485	MCF-7	breast:	n/a	chr14:103851668-103851677
45	POLR2A	chr14:103850831-103852743	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr14:103851231-103853615	PBDE	blood:	n/a	n/a
47	ELF1	chr14:103851166-103852782	GM12878	blood:	n/a	chr14:103851786-103851795 chr14:103851781-103851793 chr14:103851704-103851713 chr14:103851967-103851976 chr14:103851963-103851972
48	STAT5A	chr14:103851157-103851612	GM12878	blood:	n/a	n/a
49	REST	chr14:103850585-103853046	H1-neurons	neurons:	n/a	chr14:103850840-103850850 chr14:103851177-103851185 chr14:103851774-103851784
50	PBX3	chr14:103851233-103851925	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:103840813..103842948-chr14:103850567..103853142,2	MCF-7	breast:
2	chr14:103851236..103854697-chr14:103993929..103996210,3	MCF-7	breast:
3	chr14:103851233..103852207-chr17:15902803..15903546,2	Hela-S3	cervix:
4	chr14:103804940..103815889-chr14:103850459..103863829,28	K562	blood:
5	chr14:103794753..103806137-chr14:103849038..103864103,36	MCF-7	breast:
6	chr14:103806698..103810659-chr14:103850742..103855221,6	MCF-7	breast:
7	chr14:103799041..103818802-chr14:103836567..103862153,82	K562	blood:
8	chr14:103827117..103828725-chr14:103849989..103851539,2	K562	blood:
9	chr14:103797262..103804754-chr14:103849003..103864058,49	MCF-7	breast:
10	chr14:31676894..31677715-chr14:103851204..103851762,2	NB4	blood:
11	chr14:103798959..103802101-chr14:103850214..103852987,6	K562	blood:

Variant related genes	Relation type
MARK3	TF binding region
ENSG00000260285	Chromatin interaction
ENSG00000092148	Chromatin interaction
ENSG00000243904	Chromatin interaction
ENSG00000166166	Chromatin interaction
ENSG00000259775	Chromatin interaction
ENSG00000214941	Chromatin interaction
ENSG00000272533	Chromatin interaction
ENSG00000011295	Chromatin interaction
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10141120	0.83[CEU][hapmap]
rs10141388	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1028613	0.84[CEU][hapmap]
rs11621037	0.84[CEU][hapmap]
rs11621510	0.81[ASN][1000 genomes]
rs11623869	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs12879085	0.88[CEU][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs12889639	0.89[ASN][1000 genomes]
rs12898029	0.88[CEU][hapmap]
rs1467561	0.84[CEU][hapmap]
rs1803283	0.84[CEU][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs1951392	0.81[ASN][1000 genomes]
rs1961600	0.81[ASN][1000 genomes]
rs1989565	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs2010281	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs2273699	0.87[CEU][hapmap]
rs2273700	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs2296484	0.84[CEU][hapmap]
rs3759577	0.85[YRI][hapmap]
rs3783394	0.88[CEU][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs3783402	0.83[CEU][hapmap]
rs3825566	0.81[ASN][1000 genomes]
rs4906321	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs6575983	0.88[CEU][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs6575984	0.81[ASN][1000 genomes]
rs7140564	0.81[ASN][1000 genomes]
rs7152202	0.84[CEU][hapmap]
rs7154246	0.81[ASN][1000 genomes]
rs7155014	0.88[CEU][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs7158144	0.80[CEU][hapmap]
rs7158822	0.83[CEU][hapmap]
rs72708854	0.81[ASN][1000 genomes]
rs8015918	0.84[TSI][hapmap]
rs9671911	0.84[CEU][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	nsv1042714	chr14:103085298-103860730	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
3	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
4	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv542200	chr14:103838939-103868007	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3759579	MARK3	cis	Thyroid	GTEx
rs3759579	CKB	cis	Skin Sun Exposed Lower leg	GTEx
rs3759579	MARK3	cis	cerebellum	SCAN
rs3759579	DYNC1H1	cis	parietal	SCAN
rs3759579	C14orf153	cis	cerebellum	SCAN
rs3759579	KLC1	cis	parietal	SCAN
rs3759579	EIF5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103850400-103851400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr14:103850400-103851400	Flanking Active TSS	Dnd41	blood
3	chr14:103850600-103851400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr14:103850600-103851400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:103850600-103851400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:103850600-103851400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr14:103850600-103851400	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr14:103850600-103851400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr14:103850600-103851400	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr14:103850600-103851400	Flanking Active TSS	GM12878-XiMat	blood
11	chr14:103850600-103851400	Flanking Active TSS	HMEC	breast
12	chr14:103850600-103851400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr14:103850600-103851600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr14:103850600-103851600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:103850800-103851400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:103850800-103851400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr14:103850800-103851400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr14:103850800-103851400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr14:103850800-103851400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr14:103850800-103851400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr14:103850800-103851400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr14:103850800-103851400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr14:103850800-103851400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr14:103850800-103851400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr14:103850800-103851400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:103850800-103851400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:103850800-103851400	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr14:103850800-103851400	Flanking Active TSS	Colonic Mucosa	Colon
29	chr14:103850800-103851400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr14:103850800-103851400	Flanking Active TSS	Fetal Intestine Large	intestine
31	chr14:103850800-103851400	Flanking Active TSS	Fetal Lung	lung
32	chr14:103850800-103851400	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr14:103850800-103851400	Flanking Active TSS	Fetal Thymus	thymus
34	chr14:103850800-103851400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr14:103850800-103851400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr14:103850800-103851400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr14:103850800-103851400	Flanking Active TSS	Spleen	Spleen
38	chr14:103850800-103851400	Flanking Active TSS	Hela-S3	cervix
39	chr14:103850800-103851400	Flanking Active TSS	NH-A	brain
40	chr14:103850800-103851400	Flanking Active TSS	NHEK	skin
41	chr14:103850800-103851600	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr14:103850800-103851600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr14:103850800-103851600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr14:103850800-103851600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr14:103850800-103851600	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr14:103850800-103851600	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr14:103850800-103851600	Flanking Active TSS	HUVEC	blood vessel
48	chr14:103850800-103851800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr14:103850800-103853600	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr14:103850800-103853600	Active TSS	Rectal Smooth Muscle	rectum

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