Variant report

Variant	rs9304101
Chromosome Location	chr18:29128045-29128046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1042769	0.92[EUR][1000 genomes]
rs10502571	1.00[CHB][hapmap]
rs11661247	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs12326068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1449077	0.92[EUR][1000 genomes]
rs1626261	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs1667212	1.00[EUR][1000 genomes]
rs1667213	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs1791174	0.93[EUR][1000 genomes]
rs1941939	0.99[EUR][1000 genomes]
rs2096919	0.99[EUR][1000 genomes]
rs2276150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704039	0.90[EUR][1000 genomes]
rs2704041	0.99[EUR][1000 genomes]
rs2848664	0.90[EUR][1000 genomes]
rs28522238	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6506931	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232391	1.00[ASN][1000 genomes]
rs8084771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8093731	1.00[CHB][hapmap]
rs9304100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9947401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949695	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949790	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9951860	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs9304101	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 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	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
5	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:29117000-29136000	Weak transcription	A549	lung
7	chr18:29120000-29129600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr18:29122000-29128800	Weak transcription	NH-A	brain
9	chr18:29122800-29131800	Weak transcription	Colonic Mucosa	Colon
10	chr18:29123400-29128200	Weak transcription	K562	blood
11	chr18:29123400-29128600	Weak transcription	Right Ventricle	heart
12	chr18:29123400-29128800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr18:29123400-29128800	Weak transcription	Fetal Stomach	stomach
14	chr18:29123400-29129800	Weak transcription	Adipose Nuclei	Adipose
15	chr18:29123600-29131200	Weak transcription	Placenta	Placenta
16	chr18:29123600-29142200	Weak transcription	Fetal Kidney	kidney
17	chr18:29126400-29128200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:29126400-29128600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr18:29126600-29128200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr18:29126600-29128400	Weak transcription	Left Ventricle	heart
21	chr18:29126600-29129000	Weak transcription	Gastric	stomach
22	chr18:29126600-29131000	Weak transcription	Liver	Liver
23	chr18:29126600-29132800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:29126600-29133800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr18:29126600-29136200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr18:29126800-29128800	Weak transcription	Fetal Intestine Small	intestine
27	chr18:29126800-29129000	Weak transcription	HepG2	liver
28	chr18:29126800-29129600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr18:29126800-29136000	Weak transcription	GM12878-XiMat	blood
30	chr18:29126800-29136200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr18:29127000-29128600	Weak transcription	Fetal Thymus	thymus
32	chr18:29127000-29128600	Weak transcription	Thymus	Thymus
33	chr18:29127000-29136200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr18:29127200-29128600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr18:29127200-29129000	Weak transcription	Fetal Intestine Large	intestine
36	chr18:29127200-29129000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr18:29127200-29129000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr18:29127200-29131600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr18:29127200-29131600	Weak transcription	Fetal Lung	lung
40	chr18:29127200-29136000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr18:29127200-29136200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr18:29127200-29136200	Weak transcription	Ovary	ovary
43	chr18:29127200-29136200	Weak transcription	Hela-S3	cervix
44	chr18:29127400-29128400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr18:29127400-29129000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr18:29127400-29129000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr18:29127400-29129000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr18:29127400-29129000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr18:29127400-29129000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr18:29127400-29129200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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