Variant report

Variant	rs68004799
Chromosome Location	chr18:12967224-12967225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12966939-12967251	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12953761..12957607-chr18:12965595..12969009,3	K562	blood:
2	chr18:12947251..12949355-chr18:12965930..12968024,2	K562	blood:
3	chr18:12965185..12967426-chr18:12971269..12974109,2	MCF-7	breast:
4	chr18:12965653..12968125-chr18:12969463..12971805,2	K562	blood:
5	chr18:12946484..12949355-chr18:12965309..12968024,3	K562	blood:
6	chr18:12966070..12968300-chr18:12972176..12974458,3	K562	blood:
7	chr18:12949844..12951460-chr18:12965641..12968240,2	K562	blood:

No data

Variant related genes	Relation type
SEH1L	TF binding region
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10163827	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080617	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080618	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11661908	0.80[ASN][1000 genomes]
rs11662634	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11664213	0.96[ASN][1000 genomes]
rs11664469	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12604538	0.81[ASN][1000 genomes]
rs12605267	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607398	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12607919	0.90[ASN][1000 genomes]
rs12953783	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12957380	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960349	0.96[ASN][1000 genomes]
rs12961596	0.97[ASN][1000 genomes]
rs12963426	0.95[ASN][1000 genomes]
rs12967249	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12970503	0.97[ASN][1000 genomes]
rs13381779	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1523064	0.85[ASN][1000 genomes]
rs17603207	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17659689	0.99[ASN][1000 genomes]
rs17659749	0.99[ASN][1000 genomes]
rs17659896	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2015763	0.85[ASN][1000 genomes]
rs2282540	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2282541	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28551661	0.95[ASN][1000 genomes]
rs28654613	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34166083	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34302481	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34765181	0.81[ASN][1000 genomes]
rs35368962	1.00[ASN][1000 genomes]
rs35563947	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809914	0.92[ASN][1000 genomes]
rs3976787	0.97[ASN][1000 genomes]
rs56263236	0.86[ASN][1000 genomes]
rs7228684	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7229869	0.85[ASN][1000 genomes]
rs7230391	0.95[ASN][1000 genomes]
rs7230435	0.83[ASN][1000 genomes]
rs7234938	0.90[ASN][1000 genomes]
rs7236710	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7237711	0.84[ASN][1000 genomes]
rs7239486	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8083401	0.90[ASN][1000 genomes]
rs8086882	0.87[ASN][1000 genomes]
rs8089724	0.97[ASN][1000 genomes]
rs8090667	0.99[ASN][1000 genomes]
rs8093236	0.90[ASN][1000 genomes]
rs8093576	0.99[ASN][1000 genomes]
rs8096860	0.85[ASN][1000 genomes]
rs8566	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9950241	0.97[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	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	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
4	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
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs68004799	CEP192	cis	Artery Tibial	GTEx
rs68004799	CEP192	cis	Thyroid	GTEx
rs68004799	CEP192	cis	Esophagus Muscularis	GTEx
rs68004799	CEP192	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12971000	Weak transcription	Ovary	ovary
2	chr18:12948800-12971600	Weak transcription	Pancreas	Pancrea
3	chr18:12948800-12976600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr18:12949000-12971600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:12949000-12975400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr18:12949200-12971600	Weak transcription	Brain Substantia Nigra	brain
8	chr18:12949200-12972000	Weak transcription	Right Ventricle	heart
9	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
10	chr18:12950000-12969600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
12	chr18:12951400-12971800	Weak transcription	Gastric	stomach
13	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr18:12951800-12978400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr18:12953200-12979000	Strong transcription	Fetal Thymus	thymus
17	chr18:12956200-12975800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr18:12957000-12968400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr18:12957200-12967600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr18:12957200-12969000	Strong transcription	Primary T cells from cord blood	blood
21	chr18:12957400-12978400	Strong transcription	Dnd41	blood
22	chr18:12958400-12967600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr18:12959000-12969000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr18:12959000-12971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr18:12959000-12972000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr18:12959200-12969200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr18:12959200-12970800	Weak transcription	Brain Germinal Matrix	brain
29	chr18:12959200-12971600	Weak transcription	Brain Angular Gyrus	brain
30	chr18:12959200-12978200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:12960400-12972400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr18:12961000-12978400	Strong transcription	Fetal Intestine Small	intestine
33	chr18:12961200-12975400	Weak transcription	Stomach Mucosa	stomach
34	chr18:12961400-12975600	Weak transcription	Right Atrium	heart
35	chr18:12961600-12971800	Weak transcription	Aorta	Aorta
36	chr18:12961600-12975400	Weak transcription	Fetal Heart	heart
37	chr18:12962200-12974000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:12962400-12969000	Strong transcription	Hela-S3	cervix
39	chr18:12962600-12968600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr18:12962600-12969000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr18:12962600-12969000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr18:12962800-12969200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:12962800-12975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:12963000-12967600	Strong transcription	Fetal Kidney	kidney
45	chr18:12963000-12968200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:12963000-12969200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr18:12963200-12968600	Strong transcription	Liver	Liver
48	chr18:12963200-12968600	Strong transcription	Fetal Muscle Leg	muscle
49	chr18:12963200-12968600	Strong transcription	Osteobl	bone
50	chr18:12963200-12968800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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