Variant report

Variant	rs8093236
Chromosome Location	chr18:12944931-12944932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12944542-12947768	K562	blood:	n/a	n/a
2	FOXA1	chr18:12944861-12945032	T-47D	breast:	n/a	n/a
3	POLR2A	chr18:12944709-12945048	HepG2	liver:	n/a	n/a
4	POLR2A	chr18:12944653-12945114	Raji	blood:	n/a	n/a
5	POLR2A	chr18:12944784-12945036	ProgFib	skin:	n/a	n/a
6	POLR2A	chr18:12944894-12944949	K562	blood:	n/a	n/a
7	POLR2A	chr18:12944825-12945300	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr18:12944660-12945106	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr18:12944661-12945134	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12944143..12946293-chr18:12947055..12949999,2	MCF-7	breast:
2	chr18:12700182..12704223-chr18:12944670..12949511,9	K562	blood:
3	chr18:12741288..12744269-chr18:12942770..12945438,2	MCF-7	breast:
4	chr18:12905939..12908311-chr18:12943241..12946202,2	K562	blood:
5	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:

No data

Variant related genes	Relation type
SEH1L	TF binding region
ENSG00000101639	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000266969	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11080617	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs11080618	0.93[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11661908	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11662766	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11664213	0.86[ASN][1000 genomes]
rs11664469	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs12604538	0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs12605189	0.80[JPT][hapmap]
rs12605267	0.88[ASN][1000 genomes]
rs12607398	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12607919	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12957380	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12960349	0.80[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12961596	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12963426	0.87[ASN][1000 genomes]
rs12970503	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1523064	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs17603207	0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs17659689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17659749	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17659896	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2015763	0.82[EUR][1000 genomes]
rs2282541	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs28551661	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28654613	0.85[ASN][1000 genomes]
rs34166083	0.90[ASN][1000 genomes]
rs34302481	0.86[ASN][1000 genomes]
rs34765181	0.83[ASN][1000 genomes]
rs35368962	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35563947	0.86[ASN][1000 genomes]
rs3809914	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3976787	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4499304	0.92[CEU][hapmap]
rs56263236	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6505772	0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs67768874	0.83[ASN][1000 genomes]
rs68004799	0.90[ASN][1000 genomes]
rs7227812	0.87[MKK][hapmap]
rs7228684	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs7229406	0.87[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7230391	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7230435	0.84[EUR][1000 genomes]
rs7234163	0.87[CEU][hapmap]
rs7234938	0.80[ASN][1000 genomes]
rs7237711	0.82[EUR][1000 genomes]
rs7239486	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8083393	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs8083401	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8086882	0.89[EUR][1000 genomes]
rs8088752	0.81[JPT][hapmap]
rs8089724	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8090667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8092888	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8093576	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8096860	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs8566	0.90[ASN][1000 genomes]
rs9950241	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	esv3450694	chr18:12933001-12955144	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs8093236	CEP192	cis	Thyroid	GTEx
rs8093236	CEP192	cis	Artery Tibial	GTEx
rs8093236	CEP192	cis	lung	GTEx
rs8093236	CEP192	cis	Adipose Subcutaneous	GTEx
rs8093236	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs8093236	CEP192	cis	Nerve Tibial	GTEx
rs8093236	CEP192	cis	cerebellum	SCAN
rs8093236	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs8093236	CEP192	cis	Esophagus Muscularis	GTEx
rs8093236	CEP192	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12938600-12946000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr18:12942800-12946400	Enhancers	Fetal Thymus	thymus
3	chr18:12943000-12946000	Enhancers	Thymus	Thymus
4	chr18:12943600-12946200	Weak transcription	NH-A	brain
5	chr18:12944400-12945600	Enhancers	Fetal Muscle Leg	muscle
6	chr18:12944600-12945000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr18:12944600-12945000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr18:12944600-12945000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr18:12944600-12945000	Enhancers	Left Ventricle	heart
10	chr18:12944600-12945000	Enhancers	Psoas Muscle	Psoas
11	chr18:12944600-12945000	Enhancers	Right Atrium	heart
12	chr18:12944600-12945000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr18:12944600-12945000	Enhancers	NHDF-Ad	bronchial
14	chr18:12944600-12945000	Flanking Active TSS	Osteobl	bone
15	chr18:12944600-12945200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr18:12944600-12945200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr18:12944600-12945200	Enhancers	Colon Smooth Muscle	Colon
18	chr18:12944600-12945200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr18:12944600-12945200	Enhancers	Stomach Mucosa	stomach
20	chr18:12944600-12945400	Enhancers	Adipose Nuclei	Adipose
21	chr18:12944600-12945400	Enhancers	NHEK	skin
22	chr18:12944600-12945800	Enhancers	Fetal Muscle Trunk	muscle
23	chr18:12944600-12946000	Enhancers	Hela-S3	cervix
24	chr18:12944600-12946000	Enhancers	HSMMtube	muscle
25	chr18:12944600-12946200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:12944600-12946200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr18:12944600-12946200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr18:12944600-12946200	Enhancers	HSMM	muscle
29	chr18:12944600-12946400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr18:12944600-12946400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr18:12944600-12946600	Enhancers	Liver	Liver
32	chr18:12944600-12946800	Enhancers	Fetal Heart	heart
33	chr18:12944800-12945000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:12944800-12945000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:12944800-12945000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:12944800-12945000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr18:12944800-12945000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr18:12944800-12945000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr18:12944800-12945000	Enhancers	Brain Anterior Caudate	brain
40	chr18:12944800-12945000	Enhancers	Brain Cingulate Gyrus	brain
41	chr18:12944800-12945000	Enhancers	Brain Hippocampus Middle	brain
42	chr18:12944800-12945000	Enhancers	Brain Substantia Nigra	brain
43	chr18:12944800-12945000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr18:12944800-12945000	Enhancers	Gastric	stomach
45	chr18:12944800-12945000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr18:12944800-12945000	Enhancers	Rectal Smooth Muscle	rectum
47	chr18:12944800-12945000	Enhancers	Spleen	Spleen
48	chr18:12944800-12945000	Enhancers	HMEC	breast
49	chr18:12944800-12945200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr18:12944800-12945400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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