Variant report

Variant	rs17270517
Chromosome Location	chr11:5382834-5382835
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5382803..5384303-chr11:62607722..62610627,2	K562	blood:
2	11:5250847-5268367..11:5380014-5384338	H1-hESC	embryonic stem cell:	embryo
3	chr11:5382303..5383283-chr3:73159952..73160632,4	NB4	blood:
4	chr11:5382283..5383303-chr3:73159935..73160633,6	HCT-116	colon:
5	chr11:5382283..5383303-chr11:62608619..62609221,10	Hela-S3	cervix:
6	11:4789513-4794705..11:5380014-5384338	H1-hESC	embryonic stem cell:	embryo
7	chr11:5382283..5383283-chr3:73160073..73160610,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000260629	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000229988	Chromatin interaction
ENSG00000223609	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000188069	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10768828	1.00[JPT][hapmap]
rs10768830	1.00[JPT][hapmap]
rs10837867	1.00[JPT][hapmap]
rs10837868	1.00[JPT][hapmap]
rs10837870	1.00[JPT][hapmap]
rs10837871	1.00[JPT][hapmap]
rs10837872	1.00[JPT][hapmap]
rs10837873	1.00[JPT][hapmap]
rs10837874	1.00[JPT][hapmap]
rs10837950	0.91[JPT][hapmap]
rs10837953	0.81[JPT][hapmap]
rs10837965	0.91[JPT][hapmap]
rs10837995	0.88[JPT][hapmap]
rs11036912	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs11036923	1.00[JPT][hapmap]
rs11036924	1.00[JPT][hapmap]
rs11036925	1.00[JPT][hapmap]
rs11036927	1.00[JPT][hapmap]
rs11036930	1.00[JPT][hapmap]
rs11036936	1.00[JPT][hapmap]
rs11036968	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11037129	0.91[JPT][hapmap]
rs11037137	0.91[JPT][hapmap]
rs11037143	0.91[JPT][hapmap]
rs11037144	0.91[JPT][hapmap]
rs11037145	0.91[JPT][hapmap]
rs11037150	0.91[JPT][hapmap]
rs11037152	0.91[JPT][hapmap]
rs11037153	0.91[JPT][hapmap]
rs11037178	0.91[JPT][hapmap]
rs11037215	0.88[JPT][hapmap]
rs11601176	0.91[JPT][hapmap]
rs11601662	0.90[JPT][hapmap]
rs11603059	1.00[JPT][hapmap]
rs11604159	0.91[JPT][hapmap]
rs11604201	0.91[JPT][hapmap]
rs11604520	0.91[JPT][hapmap]
rs11604556	0.91[JPT][hapmap]
rs11604883	0.90[JPT][hapmap]
rs11607365	1.00[JPT][hapmap]
rs11826532	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12273734	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12275713	1.00[JPT][hapmap]
rs12360697	0.91[JPT][hapmap]
rs12364011	0.91[JPT][hapmap]
rs12365474	0.91[JPT][hapmap]
rs12794414	0.81[EUR][1000 genomes]
rs12796030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12801179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12802814	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12803469	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16913820	0.91[JPT][hapmap]
rs17270776	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17270818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17270832	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17270894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17271552	0.91[JPT][hapmap]
rs17271573	0.82[JPT][hapmap]
rs17355388	0.88[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17355605	0.91[JPT][hapmap]
rs17356445	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17356507	0.91[JPT][hapmap]
rs17356535	0.91[JPT][hapmap]
rs1846319	0.90[JPT][hapmap]
rs1846320	0.91[JPT][hapmap]
rs1909257	0.91[JPT][hapmap]
rs2340316	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2467229	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2467232	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2647600	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2647601	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2647604	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647605	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647606	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723380	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2723387	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2736553	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2736554	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2736555	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2736557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2736560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2736561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2736562	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2736563	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736564	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4078480	0.91[JPT][hapmap]
rs4255565	1.00[JPT][hapmap]
rs4269953	0.91[JPT][hapmap]
rs4304811	1.00[JPT][hapmap]
rs4312094	0.84[JPT][hapmap]
rs4326830	1.00[JPT][hapmap]
rs4345997	0.90[JPT][hapmap]
rs4463873	0.91[JPT][hapmap]
rs4492850	0.91[JPT][hapmap]
rs4495917	1.00[JPT][hapmap]
rs4623930	0.91[JPT][hapmap]
rs4910551	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs4910552	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910757	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910763	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910765	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910767	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910768	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910770	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910771	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4910777	0.84[ASN][1000 genomes]
rs5024037	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6578611	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs7106330	0.91[JPT][hapmap]
rs7109909	1.00[JPT][hapmap]
rs7113291	0.91[JPT][hapmap]
rs7114155	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7116471	0.91[JPT][hapmap]
rs715792	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728925	0.91[JPT][hapmap]
rs7483786	0.91[JPT][hapmap]
rs7929631	1.00[JPT][hapmap]
rs7930818	0.90[JPT][hapmap]
rs7942877	0.88[JPT][hapmap]
rs884222	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9704788	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524400	chr11:5328361-5416622	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers 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 miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv18780	chr11:5372010-5384809	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1829102	chr11:5373646-5383453	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
7	esv1828484	chr11:5374268-5386668	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1829886	chr11:5374268-5386668	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv1826272	chr11:5375383-5383341	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
10	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
11	esv1832580	chr11:5376038-5383707	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
12	nsv983147	chr11:5376861-5392760	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv18784	chr11:5382725-5384075	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv21298	chr11:5382725-5385843	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv553233	chr11:5382771-5383587	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
16	nsv553234	chr11:5382771-5383778	Enhancers Genic enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
17	esv997323	chr11:5382785-5383930	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17270517	OR52E4	cis	cerebellum	SCAN
rs17270517	OR56B1	cis	lymphoblastoid	seeQTL
rs17270517	TRIM66	cis	cerebellum	SCAN
rs17270517	TRIM22	cis	parietal	SCAN
rs17270517	KRTAP5-2	cis	cerebellum	SCAN
rs17270517	RIC3	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5382600-5383200	Strong transcription	K562	blood
2	chr11:5382600-5383600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:5382600-5384000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:5382800-5384000	Enhancers	Hela-S3	cervix
5	chr11:5382800-5384200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:5382800-5385600	Enhancers	NHDF-Ad	bronchial

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