Variant report

Variant	rs6506902
Chromosome Location	chr18:28825079-28825080
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	chr18:28821038..28822802-chr18:28823985..28826014,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10502561	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10502562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10502563	1.00[AMR][1000 genomes]
rs10502564	1.00[AFR][1000 genomes]
rs1346166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1365291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16959853	0.82[AFR][1000 genomes]
rs16961508	1.00[AMR][1000 genomes]
rs16961510	0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961517	1.00[AMR][1000 genomes]
rs16961522	1.00[AMR][1000 genomes]
rs16961523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961528	1.00[AMR][1000 genomes]
rs16961531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961539	1.00[AMR][1000 genomes]
rs16961544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16961547	0.82[AFR][1000 genomes]
rs16961551	0.82[AFR][1000 genomes]
rs16961553	0.82[AFR][1000 genomes]
rs16961554	0.82[AFR][1000 genomes]
rs16961556	0.82[AFR][1000 genomes]
rs16961558	0.82[AFR][1000 genomes]
rs35162901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58788919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59401819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60163794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60546751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60880428	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61049172	1.00[AMR][1000 genomes]
rs7241480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7241623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7241921	0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7242340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7242348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8086759	0.82[AFR][1000 genomes]
rs8095737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3360998	chr18:28693111-28881812	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28820200-28826000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr18:28820600-28828000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr18:28820800-28826200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr18:28821200-28826000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr18:28821400-28825200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:28822200-28826800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr18:28823200-28826000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr18:28823600-28825200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr18:28823600-28825400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr18:28823600-28825400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr18:28823600-28825400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr18:28823600-28825800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr18:28823800-28825200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:28823800-28825200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr18:28823800-28825200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr18:28823800-28825200	Flanking Active TSS	Liver	Liver
17	chr18:28823800-28825200	Flanking Active TSS	NHEK	skin
18	chr18:28823800-28825400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr18:28823800-28826000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr18:28824000-28825400	Flanking Active TSS	A549	lung
21	chr18:28824000-28826200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr18:28824200-28825400	Enhancers	HUVEC	blood vessel
23	chr18:28824200-28826000	Enhancers	Fetal Lung	lung
24	chr18:28824200-28826400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr18:28824200-28827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:28824200-28827600	Weak transcription	Pancreas	Pancrea
27	chr18:28824400-28825400	Enhancers	NH-A	brain
28	chr18:28824600-28825200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr18:28824600-28825200	Flanking Active TSS	Fetal Intestine Large	intestine
30	chr18:28824600-28825200	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr18:28824600-28825400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:28824600-28825400	Active TSS	Duodenum Mucosa	Duodenum
33	chr18:28824600-28825400	Flanking Active TSS	GM12878-XiMat	blood
34	chr18:28824600-28825800	Weak transcription	Colonic Mucosa	Colon
35	chr18:28824600-28826000	Enhancers	Brain Germinal Matrix	brain
36	chr18:28824800-28825200	Active TSS	Brain Cingulate Gyrus	brain
37	chr18:28824800-28825200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr18:28824800-28825200	Flanking Active TSS	Fetal Kidney	kidney
39	chr18:28824800-28825200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr18:28824800-28825200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr18:28824800-28825200	Active TSS	Right Atrium	heart
42	chr18:28824800-28825200	Enhancers	Small Intestine	intestine
43	chr18:28824800-28825200	Flanking Active TSS	Stomach Mucosa	stomach
44	chr18:28824800-28825200	Flanking Active TSS	Hela-S3	cervix
45	chr18:28824800-28825200	Flanking Active TSS	HMEC	breast
46	chr18:28824800-28830200	Weak transcription	Left Ventricle	heart
47	chr18:28825000-28825200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr18:28825000-28825200	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr18:28825000-28825200	Active TSS	Brain Hippocampus Middle	brain
50	chr18:28825000-28825200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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