Variant report

Variant	rs1042769
Chromosome Location	chr18:29125854-29125855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11661247	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12326068	0.89[CEU][hapmap];0.99[EUR][1000 genomes]
rs1449077	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791174	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1941939	0.90[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096919	0.90[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276150	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs2704039	0.90[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2704041	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2848664	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28522238	0.91[EUR][1000 genomes]
rs6506931	0.92[EUR][1000 genomes]
rs8084771	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs9304100	0.81[EUR][1000 genomes]
rs9304101	0.92[EUR][1000 genomes]
rs9947401	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs9949695	0.88[EUR][1000 genomes]
rs9949790	0.88[EUR][1000 genomes]
rs9951860	0.91[EUR][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
rs1042769	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
3	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
12	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr18:29105200-29127600	Weak transcription	Fetal Heart	heart
14	chr18:29111000-29127200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr18:29111000-29127400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:29113600-29126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr18:29114600-29127400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:29115200-29127200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:29117000-29136000	Weak transcription	A549	lung
20	chr18:29118000-29127400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr18:29118000-29127600	Strong transcription	NHEK	skin
22	chr18:29118400-29126800	Strong transcription	GM12878-XiMat	blood
23	chr18:29119800-29127800	Weak transcription	Fetal Muscle Leg	muscle
24	chr18:29120000-29127800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr18:29120000-29129600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr18:29122000-29128800	Weak transcription	NH-A	brain
27	chr18:29122800-29126800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr18:29122800-29131800	Weak transcription	Colonic Mucosa	Colon
29	chr18:29123000-29126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr18:29123200-29126000	Weak transcription	Gastric	stomach
31	chr18:29123400-29126000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:29123400-29126000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr18:29123400-29126000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr18:29123400-29126000	Weak transcription	Ovary	ovary
35	chr18:29123400-29126000	Weak transcription	Thymus	Thymus
36	chr18:29123400-29126000	Weak transcription	Hela-S3	cervix
37	chr18:29123400-29126600	Weak transcription	Fetal Lung	lung
38	chr18:29123400-29128200	Weak transcription	K562	blood
39	chr18:29123400-29128600	Weak transcription	Right Ventricle	heart
40	chr18:29123400-29128800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr18:29123400-29128800	Weak transcription	Fetal Stomach	stomach
42	chr18:29123400-29129800	Weak transcription	Adipose Nuclei	Adipose
43	chr18:29123600-29126000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr18:29123600-29131200	Weak transcription	Placenta	Placenta
45	chr18:29123600-29142200	Weak transcription	Fetal Kidney	kidney
46	chr18:29123800-29126000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr18:29123800-29126000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:29123800-29126000	Weak transcription	Fetal Intestine Small	intestine
49	chr18:29123800-29128000	Weak transcription	Pancreas	Pancrea
50	chr18:29124400-29127200	Strong transcription	Rectal Mucosa Donor 29	rectum

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