Variant report

Variant	rs2290128
Chromosome Location	chr18:29121488-29121489
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	chr18:29076759..29079471-chr18:29120956..29123046,2	K562	blood:
2	chr18:29076759..29079686-chr18:29120619..29123046,2	K562	blood:

Variant related genes	Relation type
ENSG00000046604	Chromatin interaction
ENSG00000266521	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10163532	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10502573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11542765	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327220	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12604517	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12605787	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12607843	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12607944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375443	0.94[EUR][1000 genomes]
rs16962075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962077	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17802774	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1791155	0.97[EUR][1000 genomes]
rs2053825	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053826	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2053827	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2096918	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2256638	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2278792	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737375	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3737378	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3829628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470222	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4471764	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55899143	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56389431	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62095191	0.99[EUR][1000 genomes]
rs62095194	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62095195	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62095196	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62095222	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62095223	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62095226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7244098	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7506013	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9807377	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9807379	0.95[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
rs2290128	DSG4	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
4	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
13	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr18:29105200-29127600	Weak transcription	Fetal Heart	heart
15	chr18:29110600-29121800	Strong transcription	Hela-S3	cervix
16	chr18:29110800-29123200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr18:29111000-29127200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr18:29111000-29127400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr18:29113000-29123800	Strong transcription	Fetal Intestine Small	intestine
20	chr18:29113600-29126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr18:29114400-29123600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr18:29114600-29127400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr18:29114800-29124000	Strong transcription	Fetal Intestine Large	intestine
24	chr18:29115200-29127200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr18:29115600-29123400	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr18:29116200-29123400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr18:29116400-29124000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr18:29117000-29121600	Weak transcription	Fetal Kidney	kidney
29	chr18:29117000-29121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:29117000-29136000	Weak transcription	A549	lung
31	chr18:29117800-29122000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr18:29118000-29123200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr18:29118000-29127400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr18:29118000-29127600	Strong transcription	NHEK	skin
35	chr18:29118200-29123600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr18:29118400-29123400	Strong transcription	Fetal Lung	lung
37	chr18:29118400-29123400	Strong transcription	Thymus	Thymus
38	chr18:29118400-29123400	Strong transcription	K562	blood
39	chr18:29118400-29124400	Strong transcription	HMEC	breast
40	chr18:29118400-29126800	Strong transcription	GM12878-XiMat	blood
41	chr18:29118600-29123400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr18:29118600-29123400	Strong transcription	Ovary	ovary
43	chr18:29118600-29123600	Strong transcription	Placenta	Placenta
44	chr18:29118600-29123800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr18:29118800-29123200	Strong transcription	Gastric	stomach
46	chr18:29118800-29123400	Strong transcription	Left Ventricle	heart
47	chr18:29118800-29123400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr18:29119000-29123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr18:29119200-29123000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr18:29119400-29123400	Strong transcription	Primary hematopoietic stem cells	blood

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