Variant report

Variant	rs2848680
Chromosome Location	chr18:29093317-29093318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29077683..29079249-chr18:29092433..29094661,2	MCF-7	breast:
2	chr18:29077877..29084482-chr18:29088955..29095937,13	K562	blood:
3	chr18:29078512..29082072-chr18:29089360..29094851,6	K562	blood:

Variant related genes	Relation type
ENSG00000046604	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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	0.93[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	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2704051	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2704052	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704053	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704055	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848681	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799310	0.92[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	0.92[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	0.82[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	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9304099	0.93[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	0.90[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	0.83[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	0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2848680	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 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	chr18:29084800-29093600	Weak transcription	Gastric	stomach
4	chr18:29087200-29096200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr18:29088000-29094200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr18:29088600-29093400	Enhancers	HMEC	breast
7	chr18:29088600-29094400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr18:29088600-29094400	Enhancers	HepG2	liver
9	chr18:29088600-29094600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr18:29088600-29095000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr18:29089600-29093400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr18:29089600-29094200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr18:29090000-29094600	Enhancers	Fetal Intestine Large	intestine
14	chr18:29090600-29094800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr18:29090800-29094000	Enhancers	Placenta	Placenta
16	chr18:29090800-29094000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr18:29091000-29093400	Enhancers	Duodenum Mucosa	Duodenum
18	chr18:29091000-29094800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr18:29091400-29093800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr18:29091400-29094600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr18:29091400-29103800	Weak transcription	Left Ventricle	heart
22	chr18:29091800-29094000	Enhancers	Right Ventricle	heart
23	chr18:29091800-29096200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:29092000-29093400	Weak transcription	Fetal Heart	heart
25	chr18:29092000-29094200	Enhancers	Fetal Intestine Small	intestine
26	chr18:29092000-29115600	Weak transcription	GM12878-XiMat	blood
27	chr18:29092200-29093400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr18:29092200-29093600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr18:29092200-29094000	Enhancers	NH-A	brain
30	chr18:29092200-29094200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr18:29092200-29094200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:29092200-29094400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr18:29092200-29097000	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr18:29092400-29094000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr18:29092400-29100400	Weak transcription	Liver	Liver
36	chr18:29092600-29093400	Weak transcription	Right Atrium	heart
37	chr18:29092600-29094000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:29092600-29094000	Enhancers	Ovary	ovary
39	chr18:29092600-29094000	Enhancers	K562	blood
40	chr18:29092600-29094200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr18:29092800-29093400	Weak transcription	Pancreas	Pancrea
42	chr18:29092800-29093800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:29092800-29093800	Flanking Active TSS	A549	lung
44	chr18:29092800-29096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:29092800-29104200	Weak transcription	Colonic Mucosa	Colon
46	chr18:29093000-29094600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr18:29093000-29100600	Weak transcription	Stomach Mucosa	stomach
48	chr18:29093200-29093400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr18:29093200-29093400	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr18:29093200-29094000	Enhancers	H9 Cell Line	embryonic stem cell

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