Variant report

Variant	rs190938
Chromosome Location	chr8:65283691-65283692
allele	A/C
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	JUND	chr8:65282965-65283928	H1-hESC	embryonic stem cell:	n/a	chr8:65283033-65283042
2	TEAD4	chr8:65283529-65284028	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr8:65281115-65284061	H1-hESC	embryonic stem cell:	n/a	chr8:65282566-65282579 chr8:65282249-65282262
4	CTBP2	chr8:65281156-65284174	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr8:65280803-65284029	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr8:65283684-65283711	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr8:65281790-65283716	H1-hESC	embryonic stem cell:	n/a	chr8:65281873-65281883
8	POLR2A	chr8:65280622-65295094	H1-neurons	neurons:	n/a	n/a
9	REST	chr8:65278315-65295919	H1-neurons	neurons:	n/a	chr8:65287965-65287979 chr8:65292640-65292660 chr8:65287971-65287980 chr8:65282886-65282899 chr8:65292640-65292653 chr8:65292646-65292660 chr8:65284165-65284179 chr8:65286571-65286584 chr8:65282249-65282262 chr8:65292655-65292668 chr8:65290755-65290773 chr8:65292648-65292658 chr8:65286394-65286407 chr8:65282341-65282354 chr8:65292640-65292660 chr8:65282879-65282892 chr8:65289131-65289149 chr8:65284167-65284175 chr8:65281972-65281982 chr8:65282341-65282354 chr8:65287965-65287985 chr8:65292645-65292654 chr8:65282976-65282989 chr8:65289117-65289137 chr8:65292641-65292659 chr8:65289117-65289131 chr8:65283924-65283937 chr8:65292640-65292649 chr8:65292640-65292660 chr8:65292652-65292665 chr8:65287965-65287985 chr8:65282155-65282168 chr8:65282155-65282168 chr8:65281962-65281975 chr8:65292643-65292656 chr8:65289117-65289137 chr8:65292643-65292656 chr8:65293231-65293249 chr8:65289121-65289134 chr8:65287003-65287017
10	MYC	chr8:65283484-65283801	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr8:65281359-65288713	H1-neurons	neurons:	n/a	n/a
12	TBP	chr8:65282910-65284024	H1-hESC	embryonic stem cell:	n/a	n/a
13	SUZ12	chr8:65282868-65287168	NT2-D1	testis:	n/a	n/a
14	YY1	chr8:65283443-65284139	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD2	chr8:65282977-65283732	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAF1	chr8:65283383-65284051	H1-neurons	neurons:	n/a	n/a
17	TAF1	chr8:65282817-65284159	H1-neurons	neurons:	n/a	n/a
18	TEAD4	chr8:65283431-65283982	H1-hESC	embryonic stem cell:	n/a	n/a
19	GTF2F1	chr8:65282945-65283901	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF143	chr8:65283592-65283990	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUN	chr8:65283617-65283785	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr8:65283352-65292354	H1-neurons	neurons:	n/a	chr8:65287965-65287979 chr8:65287971-65287980 chr8:65284165-65284179 chr8:65286571-65286584 chr8:65290755-65290773 chr8:65286394-65286407 chr8:65289131-65289149 chr8:65284167-65284175 chr8:65287965-65287985 chr8:65289117-65289137 chr8:65289117-65289131 chr8:65283924-65283937 chr8:65287965-65287985 chr8:65289117-65289137 chr8:65289121-65289134 chr8:65287003-65287017

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:65283649-65283699	NT2-D1	testis:	n/a
2	chr8:65283649-65283699	ECC-1	luminal epithelium:	n/a
3	chr8:65283649-65283699	HL-60	blood:	n/a
4	chr8:65283649-65283699	HCM	heart:	n/a
5	chr8:65283649-65283699	HUVEC	blood vessel:	n/a
6	chr8:65283649-65283699	SK-N-SH	brain:	n/a
7	chr8:65283649-65283699	AG04449	skin:	fetal
8	chr8:65283649-65283699	SK-N-SH_RA	brain:	n/a
9	chr8:65283649-65283699	GM06990	blood:	n/a
10	chr8:65283649-65283699	Hela-S3	cervix:	n/a
11	chr8:65283649-65283699	HRPEpiC	eye:	n/a
12	chr8:65283649-65283699	AG10803	skin:	n/a
13	chr8:65283649-65283699	AG04450	lung:	fetal
14	chr8:65283649-65283699	PFSK-1	brain:	n/a
15	chr8:65283649-65283699	BE2_C	brain:	n/a
16	chr8:65283649-65283699	MCF-7	breast:	n/a
17	chr8:65283649-65283699	HRCEpiC	kidney:	n/a
18	chr8:65283649-65283699	Jurkat	blood:	n/a
19	chr8:65283649-65283699	U87	brain:	n/a
20	chr8:65283649-65283699	IMR90	lung:	fetal
21	chr8:65283649-65283699	HNPCEpiC	eye:	n/a
22	chr8:65283649-65283699	HCPEpiC	choroid plexus:	n/a
23	chr8:65283649-65283699	GM12891	blood:	n/a
24	chr8:65283649-65283699	HAEpiC	amniotic membrane:	n/a
25	chr8:65283649-65283699	AG09309	skin:	n/a
26	chr8:65283649-65283699	HCF	heart:	n/a
27	chr8:65283649-65283699	HIPEpiC	eye:	n/a
28	chr8:65283649-65283699	K562	blood:	n/a
29	chr8:65283649-65283699	LNCaP	prostate:	n/a
30	chr8:65283649-65283699	SAEC	small airway:	n/a
31	chr8:65283649-65283699	GM12878	blood:	n/a
32	chr8:65283649-65283699	NHDF-neo	bronchial:	n/a
33	chr8:65283649-65283699	RPTEC	kidney:	n/a
34	chr8:65283649-65283699	ProgFib	skin:	n/a
35	chr8:65283649-65283699	ovcar-3	ovarian:	n/a
36	chr8:65283649-65283699	SK-N-MC	brain:	n/a
37	chr8:65283649-65283699	HPAEpiC	pulmonary alveolar:	n/a
38	chr8:65283649-65283699	HEK293	kidney:	embryo
39	chr8:65283649-65283699	NHBE	bronchial:	n/a
40	chr8:65283649-65283699	SKMC	muscle:	n/a
41	chr8:65283649-65283699	Hepatocyte	liver:	n/a
42	chr8:65283649-65283699	Caco-2	colon:	n/a
43	chr8:65283649-65283699	NH-A	brain:	n/a
44	chr8:65283649-65283699	CMK	blood:	n/a
45	chr8:65283649-65283699	PrEC	prostate:	n/a
46	chr8:65283649-65283699	HEEpiC	esophagus:	n/a
47	chr8:65283649-65283699	AoSMC	blood vessel:	n/a
48	chr8:65283649-65283699	MCF10A-Er-Src	breast:	n/a
49	chr8:65283649-65283699	BJ	skin:	n/a
50	chr8:65283649-65283699	A549	lung:	n/a

Variant related genes	Relation type
ENSG00000253554	TF binding region
LINC00966	TF binding region
ENSG00000253554	CpG island
LINC00966	CpG island

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2577888	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298204	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298205	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298208	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv948343	chr8:64804219-65328394	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv534001	chr8:64992196-65798776	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1031877	chr8:65240464-65291136	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1825065	chr8:65244654-65311200	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	esv3355215	chr8:65281423-65284271	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island	2 gene(s)	inside rSNPs	n/a
6	nsv523097	chr8:65283691-65295491	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs190938	ADHFE1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:65281000-65284200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:65281200-65283800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:65281200-65283800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr8:65281200-65283800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr8:65281200-65283800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr8:65281200-65283800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:65281200-65284000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr8:65281200-65284200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr8:65281600-65284600	Bivalent Enhancer	Liver	Liver
10	chr8:65281800-65284000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr8:65282000-65284200	Active TSS	Fetal Brain Female	brain
12	chr8:65282000-65285400	Enhancers	Fetal Brain Male	brain
13	chr8:65282200-65283800	Bivalent Enhancer	Lung	lung
14	chr8:65282400-65283800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr8:65282600-65283800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr8:65282600-65284600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr8:65282600-65286200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr8:65282800-65289200	Weak transcription	Gastric	stomach
19	chr8:65283000-65283800	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:65283000-65283800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr8:65283200-65284000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr8:65283200-65284600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:65283200-65284800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
24	chr8:65283200-65285200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
25	chr8:65283400-65283800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
26	chr8:65283400-65284000	Bivalent Enhancer	Spleen	Spleen
27	chr8:65283400-65285000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:65283400-65285400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:65283600-65283800	Bivalent Enhancer	Psoas Muscle	Psoas
30	chr8:65283600-65283800	Bivalent Enhancer	Right Ventricle	heart
31	chr8:65283600-65284000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr8:65283600-65284200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:65283600-65284200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr8:65283600-65285000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr8:65283600-65286000	Weak transcription	Right Atrium	heart

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