Variant report

Variant	rs16961613
Chromosome Location	chr18:28858789-28858790
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28855249..28856898-chr18:28857462..28860362,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1365290	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961568	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16961573	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16961579	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16961588	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16961589	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16961590	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16961592	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16961601	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961605	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961609	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16961641	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16961648	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs16961657	1.00[CEU][hapmap]
rs16961679	1.00[CEU][hapmap]
rs17728162	0.81[ASN][1000 genomes]
rs17728400	0.88[EUR][1000 genomes]
rs17801172	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17801274	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912319	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56697971	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59592286	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59593146	0.88[EUR][1000 genomes]
rs59844732	0.82[AMR][1000 genomes]
rs60220975	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62087706	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62087750	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087751	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087754	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087755	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087756	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62088669	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62088670	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62088672	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62088673	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62088674	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62088676	0.82[EUR][1000 genomes]
rs62088713	0.88[EUR][1000 genomes]
rs6506905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7234474	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237750	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8096678	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9966811	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	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
3	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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28853800-28859400	Enhancers	HepG2	liver
2	chr18:28855400-28860800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr18:28856000-28860400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr18:28856000-28861200	Weak transcription	Left Ventricle	heart
5	chr18:28857000-28859600	Enhancers	Stomach Mucosa	stomach
6	chr18:28858200-28858800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr18:28858200-28858800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr18:28858200-28859800	Enhancers	Fetal Intestine Small	intestine
9	chr18:28858400-28858800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr18:28858400-28858800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr18:28858400-28858800	Enhancers	Duodenum Mucosa	Duodenum
12	chr18:28858400-28858800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr18:28858400-28858800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr18:28858400-28859000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr18:28858400-28859200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr18:28858400-28859400	Enhancers	Fetal Intestine Large	intestine
17	chr18:28858600-28858800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr18:28858600-28858800	Enhancers	Esophagus	oesophagus
19	chr18:28858600-28858800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr18:28858600-28859000	Enhancers	H9 Cell Line	embryonic stem cell
21	chr18:28858600-28859000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr18:28858600-28859000	Enhancers	Hela-S3	cervix

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