Variant report

Variant	rs2682050
Chromosome Location	chr15:56542223-56542224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56541414..56543622-chr15:56724476..56727386,2	K562	blood:
2	chr15:56536983..56539715-chr15:56539921..56543667,5	K562	blood:
3	chr15:56540966..56543133-chr15:56718827..56720916,2	MCF-7	breast:
4	chr15:56505235..56506944-chr15:56541273..56542903,2	K562	blood:
5	chr15:56494171..56496972-chr15:56541763..56543619,2	K562	blood:

Variant related genes	Relation type
ENSG00000138587	Chromatin interaction

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

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

rs_ID	r²[population]
rs10152826	0.91[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs10162834	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10163161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10438327	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[LWK][hapmap];0.90[YRI][hapmap]
rs11632218	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11853962	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap]
rs11855937	0.81[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap]
rs11858489	0.81[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap]
rs12899534	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12901182	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs12908839	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs13379820	0.89[YRI][hapmap]
rs17238601	1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[YRI][hapmap]
rs17238691	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs17819384	0.87[LWK][hapmap]
rs2465405	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[ASN][1000 genomes]
rs2682031	0.85[JPT][hapmap]
rs2682048	0.89[ASN][1000 genomes]
rs2682055	0.87[ASN][1000 genomes]
rs2713937	0.83[JPT][hapmap]
rs2718934	0.83[CHB][hapmap]
rs2718947	0.82[ASN][1000 genomes]
rs2725871	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs28621861	0.80[ASN][1000 genomes]
rs34361729	0.85[EUR][1000 genomes]
rs35187662	0.82[ASN][1000 genomes]
rs4774854	0.91[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap]
rs56306844	0.92[EUR][1000 genomes]
rs62044097	0.89[EUR][1000 genomes]
rs62047374	0.81[EUR][1000 genomes]
rs6493844	0.82[ASN][1000 genomes]
rs7163807	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs748344	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap]
rs8032826	0.82[ASN][1000 genomes]
rs8041422	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2682050	USP8	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56538200-56546600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:56538400-56544000	Weak transcription	Fetal Brain Male	brain
3	chr15:56538400-56546000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:56538600-56543400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:56538800-56544000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:56538800-56544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:56538800-56546400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:56538800-56546600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:56540600-56543200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:56540800-56544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:56541200-56543000	Weak transcription	K562	blood
12	chr15:56541200-56543800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:56541400-56543800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:56541400-56543800	Weak transcription	Stomach Mucosa	stomach
15	chr15:56541400-56544200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:56541600-56544000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:56542200-56542400	Enhancers	Fetal Intestine Small	intestine
18	chr15:56542200-56542400	Enhancers	Rectal Mucosa Donor 31	rectum

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