Variant report

Variant	rs2555576
Chromosome Location	chr8:67345621-67345622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:67344298-67346769	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr8:67344345-67345840	HepG2	liver:	n/a	n/a
3	POLR2A	chr8:67344300-67345901	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr8:67345093-67346806	K562	blood:	n/a	n/a
5	POLR2A	chr8:67343537-67346745	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr8:67345566-67346229	HepG2	liver:	n/a	n/a
7	MXI1	chr8:67343902-67345643	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr8:67344228-67345632	GM12878	blood:	n/a	n/a
9	POLR2A	chr8:67344346-67345860	GM12878	blood:	n/a	n/a
10	POLR2A	chr8:67344136-67346344	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr8:67344418-67347661	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:67023862..67029462-chr8:67339600..67346087,12	MCF-7	breast:
2	chr8:67345421..67347646-chr8:67424128..67426947,2	MCF-7	breast:
3	chr8:66753039..66754980-chr8:67343764..67346186,2	K562	blood:
4	chr8:67344117..67347389-chr8:67347651..67352093,4	MCF-7	breast:
5	chr8:67038868..67041219-chr8:67343383..67346327,3	MCF-7	breast:
6	chr8:67344979..67348651-chr8:67356606..67358747,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000246145	TF binding region
ENSG00000253190	Chromatin interaction
ENSG00000205268	Chromatin interaction
ENSG00000147576	Chromatin interaction
ENSG00000147573	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17404672	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17405528	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2114487	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2433593	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2433594	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2433596	1.00[CHD][hapmap]
rs2465983	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2555563	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2555564	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2555567	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2555573	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap]
rs2555579	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2555586	1.00[CHD][hapmap]
rs2555588	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2555589	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2718989	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2718997	0.93[CEU][hapmap]
rs2718998	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.89[AMR][1000 genomes]
rs56256543	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57935379	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60331121	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62511170	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62511216	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62511944	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62511945	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62511947	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7014306	0.93[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7015637	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73691528	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7835343	0.83[AMR][1000 genomes];0.88[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	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	esv3414665	chr8:66936816-67381935	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2555576	ADHFE1	cis	Thyroid	GTEx
rs2555576	ADHFE1	cis	Esophagus Mucosa	GTEx
rs2555576	ADHFE1	cis	parietal	SCAN
rs2555576	ADHFE1	cis	multi-tissue	Pritchard
rs2555576	ADHFE1	cis	cerebellum	SCAN
rs2555576	ADHFE1	cis	Artery Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:67340600-67345800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr8:67341200-67345800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr8:67344400-67345800	Genic enhancers	K562	blood
4	chr8:67344400-67346200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:67345000-67345800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr8:67345000-67345800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr8:67345000-67345800	Flanking Active TSS	Liver	Liver
8	chr8:67345000-67346800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr8:67345000-67347200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr8:67345200-67345800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:67345200-67345800	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr8:67345200-67345800	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr8:67345200-67345800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr8:67345200-67345800	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr8:67345200-67345800	Flanking Active TSS	GM12878-XiMat	blood
16	chr8:67345200-67346000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:67345200-67346200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr8:67345200-67346400	Flanking Active TSS	Fetal Heart	heart
19	chr8:67345200-67351000	Weak transcription	Hela-S3	cervix
20	chr8:67345400-67345800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:67345400-67345800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr8:67345400-67345800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr8:67345400-67345800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr8:67345400-67345800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr8:67345400-67345800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr8:67345400-67345800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:67345400-67345800	Enhancers	NHEK	skin
28	chr8:67345400-67346000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr8:67345400-67346000	Enhancers	HMEC	breast
30	chr8:67345400-67346200	Genic enhancers	A549	lung
31	chr8:67345400-67346200	Genic enhancers	HSMM	muscle
32	chr8:67345400-67346400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr8:67345400-67346400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr8:67345400-67346400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr8:67345400-67347800	Enhancers	Fetal Intestine Small	intestine
36	chr8:67345400-67347800	Weak transcription	NH-A	brain
37	chr8:67345400-67348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:67345400-67348800	Weak transcription	Primary B cells from cord blood	blood
39	chr8:67345400-67348800	Enhancers	Fetal Intestine Large	intestine
40	chr8:67345400-67349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr8:67345400-67349400	Weak transcription	Fetal Stomach	stomach
42	chr8:67345400-67349800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr8:67345400-67350600	Weak transcription	Fetal Brain Female	brain
44	chr8:67345400-67350800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr8:67345400-67350800	Weak transcription	Stomach Mucosa	stomach
46	chr8:67345600-67345800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr8:67345600-67345800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr8:67345600-67345800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr8:67345600-67345800	Enhancers	Primary T cells from cord blood	blood
50	chr8:67345600-67345800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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