Variant report

Variant	rs804290
Chromosome Location	chr8:11616836-11616837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:11616708-11616854	GM19238	blood:	n/a	n/a
2	CTCF	chr8:11616707-11616867	MCF-7	breast:	n/a	n/a
3	CTCF	chr8:11616708-11616844	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr8:11616713-11616847	GM12878	blood:	n/a	n/a
5	CTCF	chr8:11616711-11616844	MCF-7	breast:	n/a	n/a
6	CTCF	chr8:11616705-11616876	MCF-7	breast:	n/a	n/a
7	CTCF	chr8:11616718-11616849	K562	blood:	n/a	n/a
8	CTCF	chr8:11616711-11616844	GM12891	blood:	n/a	n/a
9	CTCF	chr8:11616708-11616836	NHEK	skin:	n/a	n/a
10	CTCF	chr8:11616708-11616868	MCF-7	breast:	n/a	n/a
11	CTCF	chr8:11616710-11616858	GM12892	blood:	n/a	n/a
12	CTCF	chr8:11616705-11616856	GM19240	blood:	n/a	n/a
13	CTCF	chr8:11616706-11616855	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:11616798-11616848	BE2_C	brain:	n/a
2	chr8:11616798-11616848	HepG2	liver:	n/a
3	chr8:11616798-11616848	PFSK-1	brain:	n/a
4	chr8:11616798-11616848	HCM	heart:	n/a
5	chr8:11616798-11616848	NT2-D1	testis:	n/a
6	chr8:11616798-11616848	Jurkat	blood:	n/a
7	chr8:11616798-11616848	PrEC	prostate:	n/a
8	chr8:11616798-11616848	AG04450	lung:	fetal
9	chr8:11616798-11616848	NH-A	brain:	n/a
10	chr8:11616798-11616848	Hepatocyte	liver:	n/a
11	chr8:11616798-11616848	GM12892	blood:	n/a
12	chr8:11616798-11616848	SK-N-MC	brain:	n/a
13	chr8:11616798-11616848	GM06990	blood:	n/a
14	chr8:11616798-11616848	AG09309	skin:	n/a
15	chr8:11616798-11616848	NHBE	bronchial:	n/a
16	chr8:11616798-11616848	ECC-1	luminal epithelium:	n/a
17	chr8:11616798-11616848	SAEC	small airway:	n/a
18	chr8:11616798-11616848	HRCEpiC	kidney:	n/a
19	chr8:11616798-11616848	HCPEpiC	choroid plexus:	n/a
20	chr8:11616798-11616848	MCF-7	breast:	n/a
21	chr8:11616798-11616848	HCF	heart:	n/a
22	chr8:11616798-11616848	AG09319	gingival:	n/a
23	chr8:11616798-11616848	BJ	skin:	n/a
24	chr8:11616798-11616848	GM12878	blood:	n/a
25	chr8:11616798-11616848	SKMC	muscle:	n/a
26	chr8:11616798-11616848	LNCaP	prostate:	n/a
27	chr8:11616798-11616848	AG04449	skin:	fetal
28	chr8:11616798-11616848	RPTEC	kidney:	n/a
29	chr8:11616798-11616848	IMR90	lung:	fetal
30	chr8:11616798-11616848	SK-N-SH_RA	brain:	n/a
31	chr8:11616798-11616848	HEEpiC	esophagus:	n/a
32	chr8:11616798-11616848	ProgFib	skin:	n/a
33	chr8:11616798-11616848	T-47D	breast:	n/a
34	chr8:11616798-11616848	HMEC	breast:	n/a
35	chr8:11616798-11616848	Caco-2	colon:	n/a
36	chr8:11616798-11616848	HCT-116	colon:	n/a
37	chr8:11616798-11616848	HRE	kidney:	n/a
38	chr8:11616798-11616848	H1-hESC	embryonic stem cell:	embryo
39	chr8:11616798-11616848	Hela-S3	cervix:	n/a
40	chr8:11616798-11616848	U87	brain:	n/a
41	chr8:11616798-11616848	AoSMC	blood vessel:	n/a
42	chr8:11616798-11616848	HNPCEpiC	eye:	n/a
43	chr8:11616798-11616848	SK-N-SH	brain:	n/a
44	chr8:11616798-11616848	HAEpiC	amniotic membrane:	n/a
45	chr8:11616798-11616848	HUVEC	blood vessel:	n/a
46	chr8:11616798-11616848	MCF10A-Er-Src	breast:	n/a
47	chr8:11616798-11616848	ovcar-3	ovarian:	n/a
48	chr8:11616798-11616848	NHDF-neo	bronchial:	n/a
49	chr8:11616798-11616848	HIPEpiC	eye:	n/a
50	chr8:11616798-11616848	NB4	blood:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11614600..11617057-chr8:11621350..11623693,3	K562	blood:

No data

Variant related genes	Relation type
C8orf49	TF binding region
C8orf49	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12156163	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36018280	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7013933	0.81[AMR][1000 genomes]
rs804279	0.91[CEU][hapmap]
rs804292	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs8191514	0.90[AMR][1000 genomes]
rs8191518	0.87[AMR][1000 genomes]
rs8191542	1.00[YRI][hapmap]
rs8191589	1.00[CEU][hapmap]
rs8191598	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv890359	chr8:11599570-11617240	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs804290	NEIL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11606200-11617400	Strong transcription	HepG2	liver
2	chr8:11607000-11622800	Weak transcription	Stomach Mucosa	stomach
3	chr8:11608800-11619400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr8:11609200-11618600	Strong transcription	Ovary	ovary
5	chr8:11610200-11618400	Strong transcription	Liver	Liver
6	chr8:11610600-11621200	Strong transcription	Fetal Intestine Small	intestine
7	chr8:11611200-11617000	Strong transcription	Placenta	Placenta
8	chr8:11611400-11618000	Strong transcription	Pancreas	Pancrea
9	chr8:11614400-11619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:11615200-11617600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr8:11615200-11618200	Strong transcription	Gastric	stomach
12	chr8:11615400-11617000	Enhancers	Right Atrium	heart
13	chr8:11615800-11617800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr8:11615800-11626800	Weak transcription	Left Ventricle	heart
15	chr8:11616200-11617400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:11616400-11617200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:11616600-11617000	Enhancers	Fetal Heart	heart
18	chr8:11616600-11617200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr8:11616600-11617200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:11616600-11617400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:11616800-11617000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr8:11616800-11617000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:11616800-11617000	Bivalent Enhancer	K562	blood
24	chr8:11616800-11617200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:11616800-11617200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr8:11616800-11617200	Enhancers	HSMMtube	muscle
27	chr8:11616800-11617400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:11616800-11617400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr8:11616800-11617400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr8:11616800-11617400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr8:11616800-11617400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:11616800-11617400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:11616800-11617400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:11616800-11617400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:11616800-11617400	Bivalent Enhancer	Adipose Nuclei	Adipose
36	chr8:11616800-11617400	Genic enhancers	Right Ventricle	heart
37	chr8:11616800-11617800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr8:11616800-11618400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr8:11616800-11618600	Weak transcription	Stomach Smooth Muscle	stomach

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