Variant report

Variant	rs7789727
Chromosome Location	chr7:102789495-102789496
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	chr7:102788937-102790515	SK-N-SH_RA	brain:	n/a	chr7:102790061-102790083 chr7:102790024-102790043 chr7:102790032-102790040 chr7:102790096-102790110 chr7:102790064-102790072 chr7:102790019-102790041 chr7:102790030-102790038 chr7:102790031-102790041
2	TBP	chr7:102789246-102790871	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:102789302-102790329	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr7:102789211-102790674	H1-hESC	embryonic stem cell:	n/a	chr7:102789601-102789613
5	YY1	chr7:102789359-102790519	ECC-1	luminal epithelium:	n/a	chr7:102790061-102790083 chr7:102790024-102790043 chr7:102790032-102790040 chr7:102790096-102790110 chr7:102790064-102790072 chr7:102790019-102790041 chr7:102790030-102790038 chr7:102790031-102790041
6	E2F4	chr7:102789143-102790226	MCF10A-Er-Src	breast:	n/a	chr7:102789601-102789613
7	RCOR1	chr7:102789200-102790958	K562	blood:	n/a	n/a
8	MAX	chr7:102789259-102790704	H1-hESC	embryonic stem cell:	n/a	n/a
9	GTF2F1	chr7:102789033-102789686	Hela-S3	cervix:	n/a	n/a
10	HDAC2	chr7:102789252-102789823	K562	blood:	n/a	n/a
11	GTF2F1	chr7:102789247-102790406	K562	blood:	n/a	n/a
12	POLR2A	chr7:102789348-102790140	A549	lung:	n/a	n/a
13	YY1	chr7:102789263-102790570	GM12891	blood:	n/a	chr7:102790061-102790083 chr7:102790024-102790043 chr7:102790032-102790040 chr7:102790096-102790110 chr7:102790064-102790072 chr7:102790019-102790041 chr7:102790030-102790038 chr7:102790031-102790041
14	MYC	chr7:102789437-102790232	MCF-7	breast:	n/a	n/a
15	FOSL2	chr7:102789297-102789829	HepG2	liver:	n/a	n/a
16	MAX	chr7:102789072-102790486	GM12878	blood:	n/a	n/a
17	TAF1	chr7:102789261-102790137	Hela-S3	cervix:	n/a	n/a
18	TCF3	chr7:102789449-102790097	GM12878	blood:	n/a	n/a
19	MYBL2	chr7:102789300-102790238	HepG2	liver:	n/a	n/a
20	CTCF	chr7:102789460-102789610	RPTEC	kidney:	n/a	n/a
21	POLR2A	chr7:102789178-102790219	H1-neurons	neurons:	n/a	n/a
22	YY1	chr7:102789265-102790592	A549	lung:	n/a	chr7:102790061-102790083 chr7:102790024-102790043 chr7:102790032-102790040 chr7:102790096-102790110 chr7:102790064-102790072 chr7:102790019-102790041 chr7:102790030-102790038 chr7:102790031-102790041
23	POU2F2	chr7:102789144-102790645	GM12878	blood:	n/a	chr7:102790481-102790488 chr7:102789224-102789234 chr7:102790386-102790399 chr7:102790480-102790491 chr7:102789224-102789234 chr7:102789225-102789235 chr7:102790384-102790398 chr7:102789222-102789237 chr7:102790386-102790399 chr7:102790474-102790496 chr7:102790386-102790399 chr7:102790305-102790313
24	POLR2A	chr7:102789250-102790473	HCT-116	colon:	n/a	n/a
25	ELF1	chr7:102789442-102790173	HepG2	liver:	n/a	n/a
26	REST	chr7:102788997-102790220	A549	lung:	n/a	n/a
27	EP300	chr7:102789378-102789861	SK-N-SH_RA	brain:	n/a	n/a
28	MAX	chr7:102789125-102790560	HCT-116	colon:	n/a	n/a
29	BRCA1	chr7:102789056-102790328	Hela-S3	cervix:	n/a	chr7:102789633-102789640
30	HEY1	chr7:102789269-102790408	K562	blood:	n/a	chr7:102789699-102789714
31	ELF1	chr7:102789430-102790294	K562	blood:	n/a	n/a
32	E2F6	chr7:102789428-102790425	K562	blood:	n/a	chr7:102789601-102789613
33	TCF7L2	chr7:102789454-102790248	HCT-116	colon:	n/a	n/a
34	IRF1	chr7:102789084-102790981	K562	blood:	n/a	chr7:102790719-102790730 chr7:102790718-102790732 chr7:102790716-102790730
35	POLR2A	chr7:102789271-102790265	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr7:102789368-102790146	A549	lung:	n/a	n/a
37	ELF1	chr7:102789304-102790289	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:102789384-102790069	GM12891	blood:	n/a	n/a
39	POLR2A	chr7:102789295-102790228	HUVEC	blood vessel:	n/a	n/a
40	EP300	chr7:102789334-102790263	GM12878	blood:	n/a	chr7:102789949-102789962 chr7:102790037-102790053
41	PML	chr7:102789310-102790251	MCF-7	breast:	n/a	n/a
42	POLR2A	chr7:102789229-102790666	HepG2	liver:	n/a	n/a
43	MAX	chr7:102789168-102790420	MCF-7	breast:	n/a	n/a
44	E2F6	chr7:102789324-102790420	H1-hESC	embryonic stem cell:	n/a	chr7:102789601-102789613
45	MAFK	chr7:102789164-102789603	K562	blood:	n/a	chr7:102789202-102789217
46	TBP	chr7:102789165-102791061	K562	blood:	n/a	n/a
47	ZBTB33	chr7:102789363-102789881	K562	blood:	n/a	chr7:102789619-102789629
48	TBP	chr7:102789295-102790079	HepG2	liver:	n/a	n/a
49	ZBTB33	chr7:102789435-102789764	A549	lung:	n/a	chr7:102789619-102789629
50	CUX1	chr7:102789139-102789610	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102789269..102791743-chr7:102791840..102795059,5	MCF-7	breast:
2	chr7:102759033..102762956-chr7:102787889..102791523,5	K562	blood:
3	chr7:102733228..102736205-chr7:102789279..102791780,2	MCF-7	breast:
4	chr7:102788448..102791390-chr7:104652074..104655160,3	K562	blood:
5	chr7:102759379..102762894-chr7:102787802..102793821,6	K562	blood:
6	chr7:102779926..102783136-chr7:102788446..102789979,3	MCF-7	breast:
7	chr7:102788463..102790768-chr7:102937238..102939346,3	K562	blood:
8	chr7:102780818..102786371-chr7:102786977..102791342,10	K562	blood:
9	chr7:102389047..102390959-chr7:102788572..102791008,2	K562	blood:
10	chr7:102788341..102791545-chr7:102935934..102939308,4	K562	blood:
11	chr7:102789004..102789710-chr7:102937583..102938403,2	MCF-7	breast:
12	chr7:102714725..102717201-chr7:102788241..102791780,5	K562	blood:
13	chr7:102714022..102717631-chr7:102788669..102792237,6	MCF-7	breast:
14	chr7:102714786..102716772-chr7:102789401..102791256,2	MCF-7	breast:
15	chr21:34144018..34144738-chr7:102788853..102789789,2	Hela-S3	cervix:

Variant related genes	Relation type
NAPEPLD	TF binding region
ENSG00000005483	Chromatin interaction
ENSG00000159086	Chromatin interaction
ENSG00000161040	Chromatin interaction
ENSG00000205930	Chromatin interaction
ENSG00000105819	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000236848	Chromatin interaction
ENSG00000224415	Chromatin interaction
ENSG00000161048	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000222011	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10234363	0.86[EUR][1000 genomes]
rs10242349	0.86[EUR][1000 genomes]
rs10249921	0.86[EUR][1000 genomes]
rs10250825	1.00[CHD][hapmap]
rs10279441	0.86[EUR][1000 genomes]
rs11982122	1.00[CHB][hapmap]
rs17136070	0.98[EUR][1000 genomes]
rs17156420	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1861731	0.89[ASW][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.84[AFR][1000 genomes]
rs1968196	0.95[EUR][1000 genomes]
rs1968197	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28397594	0.93[EUR][1000 genomes]
rs28675125	0.86[EUR][1000 genomes]
rs3864442	0.95[EUR][1000 genomes]
rs3959192	0.98[EUR][1000 genomes]
rs57770439	0.98[EUR][1000 genomes]
rs58202498	0.98[EUR][1000 genomes]
rs58418722	0.86[EUR][1000 genomes]
rs58443652	0.93[EUR][1000 genomes]
rs59245803	0.98[EUR][1000 genomes]
rs60020835	0.98[EUR][1000 genomes]
rs60080018	0.98[EUR][1000 genomes]
rs60366734	0.98[EUR][1000 genomes]
rs60383417	0.98[EUR][1000 genomes]
rs6960317	1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6975450	0.89[EUR][1000 genomes]
rs6978467	0.93[EUR][1000 genomes]
rs6978540	0.91[EUR][1000 genomes]
rs6978608	0.93[EUR][1000 genomes]
rs6979451	0.93[EUR][1000 genomes]
rs7801094	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7810936	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7789727	NAPEPLD	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102786000-102790200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:102786200-102790400	Active TSS	Brain Hippocampus Middle	brain
3	chr7:102786200-102790400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr7:102786200-102790400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:102786400-102790200	Active TSS	Aorta	Aorta
6	chr7:102786400-102790200	Active TSS	Brain Cingulate Gyrus	brain
7	chr7:102786600-102790200	Active TSS	Stomach Smooth Muscle	stomach
8	chr7:102786800-102790000	Active TSS	Fetal Intestine Small	intestine
9	chr7:102786800-102790200	Active TSS	Duodenum Mucosa	Duodenum
10	chr7:102786800-102790400	Active TSS	Brain Angular Gyrus	brain
11	chr7:102786800-102790400	Active TSS	Brain Anterior Caudate	brain
12	chr7:102786800-102790400	Active TSS	Brain Substantia Nigra	brain
13	chr7:102787000-102790200	Active TSS	Stomach Mucosa	stomach
14	chr7:102787000-102790200	Active TSS	NHLF	lung
15	chr7:102787000-102790400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:102787000-102790400	Active TSS	Right Atrium	heart
17	chr7:102787200-102789600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:102787200-102790000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:102787200-102790000	Active TSS	Fetal Stomach	stomach
20	chr7:102787200-102790000	Active TSS	NHEK	skin
21	chr7:102787200-102790200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:102787200-102790200	Active TSS	Muscle Satellite Cultured Cells	--
23	chr7:102787200-102790200	Active TSS	Fetal Kidney	kidney
24	chr7:102787200-102790200	Active TSS	GM12878-XiMat	blood
25	chr7:102787200-102790400	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr7:102787200-102790400	Active TSS	Ovary	ovary
27	chr7:102787200-102790600	Active TSS	Fetal Brain Female	brain
28	chr7:102787200-102791400	Active TSS	Colonic Mucosa	Colon
29	chr7:102787400-102790000	Active TSS	K562	blood
30	chr7:102787400-102790000	Active TSS	NH-A	brain
31	chr7:102787400-102790200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:102787600-102790200	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr7:102787600-102790200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:102787600-102790200	Active TSS	Osteobl	bone
35	chr7:102787800-102789600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:102787800-102789800	Active TSS	HMEC	breast
37	chr7:102787800-102790000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:102787800-102790000	Active TSS	Fetal Intestine Large	intestine
39	chr7:102787800-102790000	Active TSS	Fetal Thymus	thymus
40	chr7:102787800-102790000	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr7:102787800-102790200	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr7:102787800-102790400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:102788000-102789600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:102788000-102789800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:102788000-102790000	Active TSS	H1 Cell Line	embryonic stem cell
46	chr7:102788000-102790000	Active TSS	A549	lung
47	chr7:102788000-102790200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr7:102788000-102790200	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr7:102788000-102790200	Active TSS	Fetal Lung	lung
50	chr7:102788000-102790600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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