Variant report

Variant	rs2788169
Chromosome Location	chr1:209373115-209373116
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209368320..209369917-chr1:209372141..209373660,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10863762	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119216	1.00[EUR][1000 genomes]
rs11119241	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093615	1.00[EUR][1000 genomes]
rs1320542	1.00[EUR][1000 genomes]
rs1933599	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933605	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933609	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1953754	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2039177	1.00[AMR][1000 genomes]
rs2095766	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2105164	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2185096	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2211046	1.00[AMR][1000 genomes]
rs2250698	1.00[AMR][1000 genomes]
rs2788157	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2788171	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2800917	1.00[AMR][1000 genomes]
rs2800918	1.00[AMR][1000 genomes]
rs2843177	1.00[AMR][1000 genomes]
rs4240830	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844773	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844777	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844778	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844788	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6665600	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6668118	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681778	1.00[EUR][1000 genomes]
rs6681976	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6682089	1.00[EUR][1000 genomes]
rs7529040	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs985777	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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209370400-209380800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209371600-209373800	Enhancers	H1 Cell Line	embryonic stem cell
3	chr1:209371800-209373600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:209372000-209373200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:209372000-209373200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:209372000-209373400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:209372000-209373600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:209372000-209374200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:209372200-209373200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:209372200-209373800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:209372400-209373200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:209372400-209373600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:209372400-209373800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:209372400-209373800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:209372600-209373200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:209372600-209373200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:209372600-209373200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:209372600-209373400	Enhancers	Fetal Brain Female	brain
19	chr1:209372800-209373200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:209372800-209373600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:209372800-209373600	Enhancers	Brain Germinal Matrix	brain
22	chr1:209372800-209373600	Enhancers	Fetal Brain Male	brain
23	chr1:209373000-209373200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:209373000-209373200	Enhancers	Rectal Mucosa Donor 29	rectum

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