Variant report

Variant	rs17864686
Chromosome Location	chr2:234591339-234591340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1018124	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs10929293	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12052787	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12053462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12463641	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12466747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12466779	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12466997	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12468356	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12468543	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12472689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12474980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12475068	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12476197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12477216	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12479045	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12479208	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs1604144	0.87[JPT][hapmap]
rs17862856	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17862857	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17862867	0.80[ASN][1000 genomes]
rs17862870	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs17862871	0.80[ASN][1000 genomes]
rs17862878	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17863773	0.82[AMR][1000 genomes]
rs17863790	0.80[ASN][1000 genomes]
rs17863791	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs17863792	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17863798	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17864684	0.81[AMR][1000 genomes]
rs17864696	0.80[ASN][1000 genomes]
rs17864705	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17868325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17868333	0.80[ASN][1000 genomes]
rs17868334	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs17868335	0.80[ASN][1000 genomes]
rs17868342	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17874943	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2003569	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs2013018	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2013021	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2013030	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2602381	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2885295	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs28898595	0.80[ASN][1000 genomes]
rs28898596	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs28898605	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs28898615	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28898621	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28899186	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28899187	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28899189	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs28946877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732218	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3732219	0.80[ASN][1000 genomes]
rs3732220	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3732221	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3755320	0.80[ASN][1000 genomes]
rs3755321	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3755322	0.80[ASN][1000 genomes]
rs3755323	0.80[ASN][1000 genomes]
rs3771342	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3796088	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3806591	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3806593	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3806594	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3806595	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3892170	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs3893334	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4233633	0.80[JPT][hapmap]
rs4485562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4556969	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4663325	0.80[JPT][hapmap]
rs4663326	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4663327	0.80[JPT][hapmap]
rs4663871	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4663877	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4663945	0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs4663964	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs4663968	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs5020121	0.80[ASN][1000 genomes]
rs6751673	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6753317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420193	0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs904855	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs904856	0.91[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv979185	chr2:234590426-234591548	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	nsv876016	chr2:234590527-234601669	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17864686	USP40	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234559800-234592800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:234588000-234593000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:234588600-234597000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:234589800-234593000	Weak transcription	A549	lung
5	chr2:234590000-234597800	Weak transcription	Colonic Mucosa	Colon
6	chr2:234590200-234591800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:234590800-234591600	Enhancers	Primary hematopoietic stem cells	blood
8	chr2:234590800-234592600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:234590800-234597400	Weak transcription	Liver	Liver
10	chr2:234590800-234599800	Weak transcription	Esophagus	oesophagus
11	chr2:234591000-234592600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:234591200-234591600	Enhancers	Primary B cells from cord blood	blood

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