Variant report

Variant	rs2704053
Chromosome Location	chr18:29095089-29095090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29094433..29096097-chr2:206236060..206237678,2	MCF-7	breast:
2	chr18:29077877..29084482-chr18:29088955..29095937,13	K562	blood:

Variant related genes	Relation type
ENSG00000046604	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1031729	0.97[ASN][1000 genomes]
rs11081701	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1350731	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1460602	0.96[ASN][1000 genomes]
rs17660585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1824477	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1841396	0.96[ASN][1000 genomes]
rs2212617	0.90[ASN][1000 genomes]
rs2212618	0.97[ASN][1000 genomes]
rs2219584	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704050	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2704051	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2704052	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704055	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848677	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848680	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848681	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799310	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4799573	0.95[ASN][1000 genomes]
rs6506927	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6506928	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7227343	0.89[ASN][1000 genomes]
rs7227984	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7231288	0.93[ASN][1000 genomes]
rs7231553	0.93[ASN][1000 genomes]
rs7232282	0.95[ASN][1000 genomes]
rs7235272	0.93[ASN][1000 genomes]
rs7236324	0.95[ASN][1000 genomes]
rs7236469	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7238729	0.95[ASN][1000 genomes]
rs7239805	0.84[ASN][1000 genomes]
rs7240824	0.81[ASN][1000 genomes]
rs7240920	0.87[ASN][1000 genomes]
rs7241107	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73414280	0.94[ASN][1000 genomes]
rs73953901	0.95[ASN][1000 genomes]
rs9304097	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304098	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9304099	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9941421	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9945031	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945420	0.85[ASN][1000 genomes]
rs9951843	0.90[ASN][1000 genomes]
rs9961910	0.91[ASN][1000 genomes]
rs9961920	0.95[ASN][1000 genomes]
rs9961925	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9962121	0.95[ASN][1000 genomes]
rs9962318	0.95[ASN][1000 genomes]
rs9962333	0.85[ASN][1000 genomes]
rs9962423	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2704053	RP11-650P15.1	cis	Thyroid	GTEx
rs2704053	DSG2	Cis_1M	lymphoblastoid	RTeQTL
rs2704053	RP11-650P15.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29080600-29100000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:29080600-29100400	Weak transcription	Fetal Thymus	thymus
3	chr18:29087200-29096200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr18:29091400-29103800	Weak transcription	Left Ventricle	heart
5	chr18:29091800-29096200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:29092000-29115600	Weak transcription	GM12878-XiMat	blood
7	chr18:29092200-29097000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr18:29092400-29100400	Weak transcription	Liver	Liver
9	chr18:29092800-29096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:29092800-29104200	Weak transcription	Colonic Mucosa	Colon
11	chr18:29093000-29100600	Weak transcription	Stomach Mucosa	stomach
12	chr18:29093200-29099800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr18:29093400-29101000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr18:29093400-29103000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:29093600-29099600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:29094000-29095400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:29094000-29095600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr18:29094000-29096400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr18:29094000-29098600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr18:29094000-29099400	Weak transcription	K562	blood
21	chr18:29094000-29099600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr18:29094000-29101000	Weak transcription	Placenta	Placenta
23	chr18:29094000-29103600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr18:29094000-29103800	Weak transcription	NH-A	brain
25	chr18:29094000-29104000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr18:29094000-29104400	Weak transcription	Fetal Heart	heart
27	chr18:29094000-29104800	Weak transcription	Ovary	ovary
28	chr18:29094000-29104800	Weak transcription	Pancreas	Pancrea
29	chr18:29094000-29110400	Weak transcription	Esophagus	oesophagus
30	chr18:29094000-29118800	Weak transcription	Gastric	stomach
31	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
32	chr18:29094200-29095400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr18:29094200-29096800	Weak transcription	Fetal Intestine Small	intestine
34	chr18:29094200-29097800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:29094200-29099800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr18:29094400-29095400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr18:29094400-29095800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr18:29094400-29099400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr18:29094400-29099600	Weak transcription	HepG2	liver
40	chr18:29094400-29100000	Weak transcription	HMEC	breast
41	chr18:29094400-29100200	Weak transcription	Hela-S3	cervix
42	chr18:29094600-29095400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr18:29094600-29096600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr18:29094600-29097600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr18:29094600-29097800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr18:29094600-29099800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr18:29094600-29099800	Weak transcription	Fetal Intestine Large	intestine
48	chr18:29094600-29099800	Weak transcription	A549	lung
49	chr18:29094800-29095200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr18:29094800-29095600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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