Variant report

Variant	rs16962077
Chromosome Location	chr18:29120437-29120438
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10163532	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10502573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11542765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327220	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12604517	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	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12607944	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375443	0.94[EUR][1000 genomes]
rs16962075	1.00[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	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2256638	1.00[EUR][1000 genomes]
rs2278792	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290128	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737375	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3737378	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3829628	1.00[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	0.90[AFR][1000 genomes];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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29094000-29121200	Weak transcription	Right Ventricle	heart
2	chr18:29096800-29121800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr18:29096800-29134600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr18:29097200-29129400	Weak transcription	Small Intestine	intestine
5	chr18:29097600-29128000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr18:29097800-29130600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:29098200-29127600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr18:29098600-29127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:29099400-29127400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr18:29099400-29128000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:29099600-29127400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr18:29099600-29128000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:29101400-29131800	Weak transcription	Stomach Mucosa	stomach
14	chr18:29103400-29128200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr18:29105200-29127600	Weak transcription	Fetal Heart	heart
16	chr18:29107200-29120800	Weak transcription	NH-A	brain
17	chr18:29110600-29121800	Strong transcription	Hela-S3	cervix
18	chr18:29110800-29123200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr18:29111000-29127200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr18:29111000-29127400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr18:29113000-29123800	Strong transcription	Fetal Intestine Small	intestine
22	chr18:29113600-29126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr18:29114400-29123600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr18:29114600-29127400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr18:29114800-29124000	Strong transcription	Fetal Intestine Large	intestine
26	chr18:29115200-29127200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr18:29115600-29123400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr18:29116200-29123400	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr18:29116400-29124000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:29117000-29121600	Weak transcription	Fetal Kidney	kidney
31	chr18:29117000-29121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:29117000-29136000	Weak transcription	A549	lung
33	chr18:29117800-29122000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr18:29118000-29123200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr18:29118000-29127400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr18:29118000-29127600	Strong transcription	NHEK	skin
37	chr18:29118200-29123600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr18:29118400-29123400	Strong transcription	Fetal Lung	lung
39	chr18:29118400-29123400	Strong transcription	Thymus	Thymus
40	chr18:29118400-29123400	Strong transcription	K562	blood
41	chr18:29118400-29124400	Strong transcription	HMEC	breast
42	chr18:29118400-29126800	Strong transcription	GM12878-XiMat	blood
43	chr18:29118600-29123400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr18:29118600-29123400	Strong transcription	Ovary	ovary
45	chr18:29118600-29123600	Strong transcription	Placenta	Placenta
46	chr18:29118600-29123800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr18:29118800-29123200	Strong transcription	Gastric	stomach
48	chr18:29118800-29123400	Strong transcription	Left Ventricle	heart
49	chr18:29118800-29123400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr18:29119000-29123400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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