Variant report

Variant	rs868546
Chromosome Location	chr8:69242537-69242538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr8:69242446-69244878	H1-hESC	embryonic stem cell:	n/a	chr8:69244450-69244464 chr8:69243753-69243764 chr8:69243453-69243464 chr8:69243196-69243205 chr8:69244457-69244470
2	KAP1	chr8:69242465-69243925	HEK293	kidney:	n/a	n/a
3	E2F6	chr8:69242454-69244094	H1-hESC	embryonic stem cell:	n/a	chr8:69242701-69242710 chr8:69242697-69242712 chr8:69242698-69242712 chr8:69243122-69243134 chr8:69242697-69242712 chr8:69242702-69242713

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:69242509-69242559	GM19239	blood:	n/a
2	chr8:69242509-69242559	GM12878	blood:	n/a
3	chr8:69242509-69242559	HEEpiC	esophagus:	n/a
4	chr8:69242509-69242559	IMR90	lung:	fetal
5	chr8:69242509-69242559	SK-N-SH	brain:	n/a
6	chr8:69242509-69242559	HPAEpiC	pulmonary alveolar:	n/a
7	chr8:69242509-69242559	HEK293	kidney:	embryo
8	chr8:69242509-69242559	PFSK-1	brain:	n/a
9	chr8:69242509-69242559	HCT-116	colon:	n/a
10	chr8:69242509-69242559	HRE	kidney:	n/a
11	chr8:69242509-69242559	AG04450	lung:	fetal
12	chr8:69242509-69242559	ProgFib	skin:	n/a
13	chr8:69242509-69242559	Hela-S3	cervix:	n/a
14	chr8:69242509-69242559	NHBE	bronchial:	n/a
15	chr8:69242509-69242559	SAEC	small airway:	n/a
16	chr8:69242509-69242559	AG09309	skin:	n/a
17	chr8:69242509-69242559	AG09319	gingival:	n/a
18	chr8:69242509-69242559	T-47D	breast:	n/a
19	chr8:69242509-69242559	H1-hESC	embryonic stem cell:	embryo
20	chr8:69242509-69242559	BE2_C	brain:	n/a
21	chr8:69242509-69242559	SKMC	muscle:	n/a
22	chr8:69242509-69242559	SK-N-MC	brain:	n/a
23	chr8:69242509-69242559	MCF-7	breast:	n/a
24	chr8:69242509-69242559	SK-N-SH_RA	brain:	n/a
25	chr8:69242509-69242559	NB4	blood:	n/a
26	chr8:69242509-69242559	GM12892	blood:	n/a
27	chr8:69242509-69242559	NHDF-neo	bronchial:	n/a
28	chr8:69242509-69242559	HMEC	breast:	n/a
29	chr8:69242509-69242559	HUVEC	blood vessel:	n/a
30	chr8:69242509-69242559	HAEpiC	amniotic membrane:	n/a
31	chr8:69242509-69242559	HCPEpiC	choroid plexus:	n/a
32	chr8:69242509-69242559	HRPEpiC	eye:	n/a
33	chr8:69242509-69242559	RPTEC	kidney:	n/a
34	chr8:69242509-69242559	AoSMC	blood vessel:	n/a
35	chr8:69242509-69242559	MCF10A-Er-Src	breast:	n/a
36	chr8:69242509-69242559	NH-A	brain:	n/a
37	chr8:69242509-69242559	Jurkat	blood:	n/a
38	chr8:69242509-69242559	AG04449	skin:	fetal
39	chr8:69242509-69242559	NT2-D1	testis:	n/a
40	chr8:69242509-69242559	ovcar-3	ovarian:	n/a
41	chr8:69242509-69242559	LNCaP	prostate:	n/a
42	chr8:69242509-69242559	HNPCEpiC	eye:	n/a
43	chr8:69242509-69242559	HCF	heart:	n/a
44	chr8:69242509-69242559	HCM	heart:	n/a
45	chr8:69242509-69242559	HL-60	blood:	n/a
46	chr8:69242509-69242559	Hepatocyte	liver:	n/a
47	chr8:69242509-69242559	HRCEpiC	kidney:	n/a
48	chr8:69242509-69242559	GM06990	blood:	n/a
49	chr8:69242509-69242559	PANC-1	pancreas:	n/a
50	chr8:69242509-69242559	U87	brain:	n/a

No data

Variant related genes	Relation type
C8orf34	TF binding region
C8orf34	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10098538	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10104993	0.80[GIH][hapmap]
rs12549988	1.00[YRI][hapmap]
rs13251356	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13257807	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13261104	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13262740	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13276394	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs13278793	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1517124	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1607144	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1971404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1971527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138677	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2176368	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6472395	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6982836	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs6991818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7000384	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7001418	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7004646	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7013597	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7015549	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7017437	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7818147	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7822588	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7823116	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7823422	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7838935	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs814441	0.91[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs814444	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs814446	0.81[JPT][hapmap]
rs814463	0.84[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	nsv1028889	chr8:69026806-69308725	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv948687	chr8:69041121-69642540	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv890979	chr8:69176154-69252417	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv890980	chr8:69181681-69252417	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3423266	chr8:69242023-69244571	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs868546	RPS20	trans	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:69242200-69243000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr8:69242200-69246200	Active TSS	Brain Anterior Caudate	brain
3	chr8:69242200-69246200	Active TSS	Fetal Brain Female	brain
4	chr8:69242400-69242600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
5	chr8:69242400-69242600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:69242400-69242600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:69242400-69242600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:69242400-69242600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
9	chr8:69242400-69242600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr8:69242400-69242600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr8:69242400-69242600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
12	chr8:69242400-69242600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:69242400-69242600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:69242400-69242600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:69242400-69242600	Enhancers	Adipose Nuclei	Adipose
16	chr8:69242400-69242600	Enhancers	Aorta	Aorta
17	chr8:69242400-69242600	Bivalent Enhancer	Fetal Kidney	kidney
18	chr8:69242400-69242600	Bivalent Enhancer	Fetal Lung	lung
19	chr8:69242400-69242600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr8:69242400-69242800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr8:69242400-69242800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr8:69242400-69242800	Active TSS	Brain Cingulate Gyrus	brain
23	chr8:69242400-69243000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:69242400-69243400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:69242400-69243400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr8:69242400-69243400	Active TSS	Brain Substantia Nigra	brain
27	chr8:69242400-69243400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
28	chr8:69242400-69244200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:69242400-69244200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:69242400-69244800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr8:69242400-69244800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:69242400-69244800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
33	chr8:69242400-69245000	Active TSS	H9 Cell Line	embryonic stem cell
34	chr8:69242400-69245000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr8:69242400-69245000	Active TSS	Brain Angular Gyrus	brain
36	chr8:69242400-69245200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:69242400-69245200	Active TSS	Brain Hippocampus Middle	brain

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