Variant report

Variant	rs17260224
Chromosome Location	chr1:209402558-209402559
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209400144..209402804-chr1:209588450..209590048,2	MCF-7	breast:
2	chr1:209393306..209397796-chr1:209399926..209403415,4	MCF-7	breast:
3	chr1:209401346..209403763-chr1:209407691..209409973,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494919	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1507332	0.87[EUR][1000 genomes]
rs1507333	0.95[EUR][1000 genomes]
rs1553623	0.87[EUR][1000 genomes]
rs17188002	0.96[ASN][1000 genomes]
rs17188016	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17188030	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17260245	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1933613	0.96[ASN][1000 genomes]
rs2055700	0.95[EUR][1000 genomes]
rs2788153	0.88[EUR][1000 genomes]
rs2800930	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4504891	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56805778	0.96[ASN][1000 genomes]
rs57720299	0.96[ASN][1000 genomes]
rs59563227	0.96[ASN][1000 genomes]
rs59658508	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6657861	0.96[ASN][1000 genomes]
rs6661882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671102	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6681844	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6687960	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73083997	0.96[ASN][1000 genomes]
rs73085905	0.96[ASN][1000 genomes]
rs73085915	0.96[ASN][1000 genomes]
rs73085919	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73085921	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73085926	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73085932	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73085944	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73085950	0.93[EUR][1000 genomes]
rs7533402	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs906352	0.92[EUR][1000 genomes]
rs949488	0.95[EUR][1000 genomes]
rs976940	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17260224	SNORD116-29	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209398600-209402600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:209400000-209402600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:209400800-209404800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:209401400-209403600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:209401600-209402800	Weak transcription	Fetal Brain Male	brain
6	chr1:209402200-209403600	Enhancers	HMEC	breast
7	chr1:209402200-209403800	Enhancers	NHEK	skin
8	chr1:209402400-209403000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:209402400-209403400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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