Variant report

Variant	rs2719008
Chromosome Location	chr8:67383784-67383785
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	JUN	chr8:67383477-67383961	Hela-S3	cervix:	n/a	n/a
2	SP1	chr8:67383487-67383990	HCT-116	colon:	n/a	n/a
3	CEBPB	chr8:67383544-67383955	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr8:67383533-67384072	MCF-7	breast:	n/a	chr8:67383800-67383808
5	EP300	chr8:67383335-67384063	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr8:67383507-67383995	Hela-S3	cervix:	n/a	n/a
7	FOS	chr8:67383518-67383915	Hela-S3	cervix:	n/a	chr8:67383695-67383706
8	EP300	chr8:67383527-67383961	Hela-S3	cervix:	n/a	n/a
9	SETDB1	chr8:67383543-67384269	U2OS	brain:	n/a	n/a
10	RXRA	chr8:67383423-67384092	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr8:67383540-67384058	MCF-7	breast:	n/a	chr8:67383800-67383808
12	GATA3	chr8:67383356-67384194	SK-N-SH	brain:	n/a	chr8:67383800-67383808
13	CBX3	chr8:67383537-67383999	HCT-116	colon:	n/a	n/a
14	FOSL2	chr8:67383512-67383969	MCF-7	breast:	n/a	n/a
15	TCF7L2	chr8:67383682-67383917	MCF-7	breast:	n/a	n/a
16	NR2F2	chr8:67383430-67384105	MCF-7	breast:	n/a	n/a
17	TEAD4	chr8:67383506-67383863	A549	lung:	n/a	n/a
18	CEBPB	chr8:67383574-67383955	IMR90	lung:	n/a	n/a
19	GATA2	chr8:67383532-67384639	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr8:67383542-67383932	HUVEC	blood vessel:	n/a	n/a
21	TCF12	chr8:67383311-67384144	SK-N-SH	brain:	n/a	n/a
22	SP1	chr8:67383397-67383998	A549	lung:	n/a	n/a
23	JUND	chr8:67383415-67384060	SK-N-SH	brain:	n/a	chr8:67383695-67383706
24	EP300	chr8:67383439-67384043	A549	lung:	n/a	n/a
25	EP300	chr8:67383364-67384080	SK-N-SH	brain:	n/a	n/a
26	GATA3	chr8:67383422-67384214	SK-N-SH	brain:	n/a	chr8:67383800-67383808
27	MAX	chr8:67383522-67383911	SK-N-SH	brain:	n/a	n/a
28	FOS	chr8:67383507-67383956	HUVEC	blood vessel:	n/a	chr8:67383695-67383706
29	FOSL2	chr8:67383417-67384072	A549	lung:	n/a	n/a
30	STAT3	chr8:67383660-67383857	MCF10A-Er-Src	breast:	n/a	n/a
31	RFX5	chr8:67383524-67383957	Hela-S3	cervix:	n/a	n/a
32	JUND	chr8:67383531-67383857	A549	lung:	n/a	chr8:67383695-67383706
33	JUN	chr8:67383632-67383815	HepG2	liver:	n/a	n/a
34	RXRA	chr8:67383465-67384102	SK-N-SH	brain:	n/a	n/a
35	YY1	chr8:67383554-67384054	SK-N-SH	brain:	n/a	n/a
36	JUND	chr8:67383429-67383974	HCT-116	colon:	n/a	chr8:67383695-67383706
37	EP300	chr8:67383520-67383907	SK-N-SH_RA	brain:	n/a	n/a
38	POLR2A	chr8:67383434-67383940	PANC-1	pancreas:	n/a	n/a
39	EP300	chr8:67383561-67383847	SK-N-SH_RA	brain:	n/a	n/a
40	POLR2A	chr8:67383769-67383879	HUVEC	blood vessel:	n/a	n/a
41	FOSL2	chr8:67383452-67383971	SK-N-SH	brain:	n/a	n/a
42	FOXM1	chr8:67383300-67384166	SK-N-SH	brain:	n/a	n/a
43	KAP1	chr8:67383560-67383939	U2OS	brain:	n/a	n/a
44	GATA3	chr8:67383558-67383942	T-47D	breast:	n/a	chr8:67383800-67383808
45	POLR2A	chr8:67383456-67383970	SK-N-SH	brain:	n/a	n/a
46	MAX	chr8:67383479-67384053	A549	lung:	n/a	n/a
47	POLR2A	chr8:67383527-67383905	PANC-1	pancreas:	n/a	n/a
48	FOSL1	chr8:67383513-67384054	HCT-116	colon:	n/a	n/a
49	JUND	chr8:67383271-67384155	SK-N-SH	brain:	n/a	chr8:67383695-67383706
50	CEBPB	chr8:67383582-67383903	A549	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADHFE1-1	chr8:67383684-67383853	XLOC_006828

Variant related genes	Relation type
C8orf46	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1030421	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1060242	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1108	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12544088	0.84[ASN][1000 genomes]
rs13682	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1978566	0.84[MEX][hapmap]
rs2059640	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059641	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2059642	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2357893	0.80[EUR][1000 genomes]
rs2357894	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2465990	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2555568	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2555569	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2555570	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2555572	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2555574	0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2719000	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2719002	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2719004	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2719005	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35352031	0.91[CHB][hapmap]
rs4737798	0.84[ASN][1000 genomes]
rs55878528	0.81[ASN][1000 genomes]
rs6993131	0.80[ASN][1000 genomes]
rs7001334	0.84[ASN][1000 genomes]
rs7005590	0.83[ASN][1000 genomes]
rs7014980	0.91[CHB][hapmap]
rs72652765	0.88[ASN][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	esv3446467	chr8:66749863-67667068	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv6236	chr8:67359312-67403981	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv465702	chr8:67375519-67385088	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv611457	chr8:67375519-67385088	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1026137	chr8:67376420-67408122	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2719008	ADHFE1	cis	Muscle Skeletal	GTEx
rs2719008	C8orf46	cis	Adipose Subcutaneous	GTEx
rs2719008	ADHFE1	cis	Nerve Tibial	GTEx
rs2719008	ADHFE1	cis	Skin Sun Exposed Lower leg	GTEx
rs2719008	C8orf46	cis	Stomach	GTEx
rs2719008	C8orf46	cis	Skin Sun Exposed Lower leg	GTEx
rs2719008	C8orf46	cis	Muscle Skeletal	GTEx
rs2719008	C8orf46	cis	multi-tissue	Pritchard
rs2719008	ADHFE1	cis	multi-tissue	Pritchard
rs2719008	MYBL1	cis	parietal	SCAN
rs2719008	C8orf46	cis	Nerve Tibial	GTEx
rs2719008	C8orf46	cis	lung	GTEx
rs2719008	C8orf46	cis	Liver	GTEx
rs2719008	ADHFE1	cis	Heart Left Ventricle	GTEx
rs2719008	ADHFE1	cis	Artery Tibial	GTEx
rs2719008	C8orf46	cis	Thyroid	GTEx
rs2719008	C8orf46	cis	Esophagus Muscularis	GTEx
rs2719008	ADHFE1	cis	parietal	SCAN
rs2719008	C8orf46	cis	Artery Tibial	GTEx
rs2719008	ADHFE1	cis	Thyroid	GTEx
rs2719008	C8orf46	cis	Esophagus Mucosa	GTEx
rs2719008	ADHFE1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:67359400-67384400	Weak transcription	Fetal Kidney	kidney
2	chr8:67364800-67384000	Weak transcription	Colon Smooth Muscle	Colon
3	chr8:67365400-67383800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:67368400-67384400	Weak transcription	Psoas Muscle	Psoas
5	chr8:67370800-67384200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:67371200-67383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr8:67371400-67384200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr8:67372800-67384400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:67372800-67395200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr8:67373000-67384400	Weak transcription	Brain Angular Gyrus	brain
11	chr8:67373800-67385400	Weak transcription	Fetal Intestine Small	intestine
12	chr8:67374800-67384600	Weak transcription	Lung	lung
13	chr8:67374800-67396800	Weak transcription	Pancreas	Pancrea
14	chr8:67375000-67384600	Weak transcription	Right Ventricle	heart
15	chr8:67376400-67383800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr8:67376400-67384200	Weak transcription	HSMM	muscle
17	chr8:67376400-67390000	Weak transcription	Fetal Heart	heart
18	chr8:67376800-67384000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr8:67376800-67384800	Weak transcription	Fetal Lung	lung
20	chr8:67377200-67389400	Weak transcription	Brain Substantia Nigra	brain
21	chr8:67379400-67383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:67379400-67383800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr8:67379600-67384200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr8:67379600-67384200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr8:67379600-67384200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr8:67379800-67384400	Weak transcription	Left Ventricle	heart
27	chr8:67380000-67386000	Weak transcription	Fetal Intestine Large	intestine
28	chr8:67380800-67384200	Weak transcription	Brain Anterior Caudate	brain
29	chr8:67380800-67405200	Weak transcription	Aorta	Aorta
30	chr8:67381000-67384200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr8:67381000-67388200	Weak transcription	Adipose Nuclei	Adipose
32	chr8:67381200-67384800	Weak transcription	Liver	Liver
33	chr8:67381600-67386200	Weak transcription	Ovary	ovary
34	chr8:67381800-67384400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:67381800-67385600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr8:67381800-67389400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr8:67382200-67384400	Enhancers	NHEK	skin
38	chr8:67382200-67384600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr8:67382200-67384800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:67382200-67384800	Enhancers	NH-A	brain
41	chr8:67382600-67386200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr8:67382800-67383800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr8:67382800-67384400	Enhancers	Osteobl	bone
44	chr8:67382800-67384600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr8:67382800-67384600	Enhancers	Placenta	Placenta
46	chr8:67382800-67384800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr8:67382800-67384800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:67382800-67384800	Enhancers	HUVEC	blood vessel
49	chr8:67382800-67384800	Enhancers	NHLF	lung
50	chr8:67382800-67385000	Enhancers	Hela-S3	cervix

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