Variant report

Variant	rs17271934
Chromosome Location	chr5:111685654-111685655
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	chr5:111685601..111687919-chr5:111689516..111692384,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10037824	1.00[ASN][1000 genomes]
rs10040749	1.00[CHD][hapmap]
rs10054560	1.00[ASN][1000 genomes]
rs10065740	1.00[ASN][1000 genomes]
rs10068493	1.00[ASN][1000 genomes]
rs10069011	1.00[ASN][1000 genomes]
rs10463433	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs10477478	1.00[ASN][1000 genomes]
rs10478073	1.00[ASN][1000 genomes]
rs1054724	1.00[CHD][hapmap]
rs1078128	1.00[ASN][1000 genomes]
rs11241153	1.00[ASN][1000 genomes]
rs11241160	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186685	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12187589	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187787	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187819	1.00[ASN][1000 genomes]
rs12187850	0.86[CEU][hapmap]
rs12188700	1.00[ASN][1000 genomes]
rs12189034	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12189437	0.93[GIH][hapmap];0.88[MEX][hapmap]
rs13153601	1.00[ASN][1000 genomes]
rs1318178	1.00[ASN][1000 genomes]
rs1366144	1.00[ASN][1000 genomes]
rs1427978	1.00[ASN][1000 genomes]
rs1524425	0.86[CEU][hapmap]
rs1554624	0.86[CEU][hapmap];0.94[TSI][hapmap]
rs1560053	1.00[ASN][1000 genomes]
rs1560054	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1560055	1.00[ASN][1000 genomes]
rs1560057	1.00[ASN][1000 genomes]
rs1560058	1.00[ASN][1000 genomes]
rs1560061	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17134319	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs17134321	0.93[CEU][hapmap]
rs17134327	0.86[CEU][hapmap];1.00[TSI][hapmap]
rs17134348	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs17343994	1.00[ASN][1000 genomes]
rs17345175	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17354763	1.00[ASN][1000 genomes]
rs17354833	1.00[ASN][1000 genomes]
rs1896620	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896621	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067096	1.00[ASN][1000 genomes]
rs2114991	1.00[CHD][hapmap]
rs2416277	1.00[ASN][1000 genomes]
rs386446	1.00[ASN][1000 genomes]
rs4292487	1.00[ASN][1000 genomes]
rs4602685	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4957632	1.00[ASN][1000 genomes]
rs4957634	1.00[ASN][1000 genomes]
rs4957636	1.00[ASN][1000 genomes]
rs4958002	1.00[ASN][1000 genomes]
rs4958003	1.00[ASN][1000 genomes]
rs4958004	1.00[ASN][1000 genomes]
rs4958009	1.00[ASN][1000 genomes]
rs4958010	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4958012	1.00[ASN][1000 genomes]
rs4958013	1.00[ASN][1000 genomes]
rs4958014	1.00[ASN][1000 genomes]
rs4958015	1.00[ASN][1000 genomes]
rs4958020	1.00[ASN][1000 genomes]
rs4958025	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs55639430	1.00[ASN][1000 genomes]
rs55650579	1.00[ASN][1000 genomes]
rs55712004	1.00[ASN][1000 genomes]
rs55796748	1.00[ASN][1000 genomes]
rs55814486	1.00[ASN][1000 genomes]
rs55829200	1.00[ASN][1000 genomes]
rs55845736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55913426	1.00[ASN][1000 genomes]
rs56108405	1.00[ASN][1000 genomes]
rs56288086	1.00[ASN][1000 genomes]
rs56293447	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307310	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56881711	1.00[ASN][1000 genomes]
rs57428532	1.00[ASN][1000 genomes]
rs59537089	1.00[ASN][1000 genomes]
rs60636568	1.00[ASN][1000 genomes]
rs61061658	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365251	1.00[ASN][1000 genomes]
rs62365255	1.00[ASN][1000 genomes]
rs62367266	1.00[ASN][1000 genomes]
rs6594566	1.00[CHD][hapmap]
rs6594574	1.00[ASN][1000 genomes]
rs6594577	1.00[ASN][1000 genomes]
rs6594588	0.93[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66521031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66537821	0.86[EUR][1000 genomes]
rs66550707	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66814803	1.00[ASN][1000 genomes]
rs66892745	1.00[ASN][1000 genomes]
rs67033649	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67586008	1.00[ASN][1000 genomes]
rs67631852	1.00[ASN][1000 genomes]
rs6863063	1.00[ASN][1000 genomes]
rs6872947	1.00[CHD][hapmap]
rs6876893	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6878117	1.00[ASN][1000 genomes]
rs6878423	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6884589	1.00[ASN][1000 genomes]
rs6893877	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6894036	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894358	0.82[EUR][1000 genomes]
rs72781655	1.00[ASN][1000 genomes]
rs72781664	1.00[ASN][1000 genomes]
rs72781668	1.00[ASN][1000 genomes]
rs72781677	1.00[ASN][1000 genomes]
rs72781678	1.00[ASN][1000 genomes]
rs72783609	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72783628	1.00[ASN][1000 genomes]
rs72783634	1.00[ASN][1000 genomes]
rs7703522	1.00[CHD][hapmap]
rs7704087	1.00[ASN][1000 genomes]
rs7706160	1.00[ASN][1000 genomes]
rs7709484	1.00[ASN][1000 genomes]
rs7710973	1.00[ASN][1000 genomes]
rs7711158	1.00[ASN][1000 genomes]
rs7714258	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs7716309	1.00[ASN][1000 genomes]
rs7716394	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7717160	1.00[CHD][hapmap]
rs7717363	1.00[ASN][1000 genomes]
rs7719346	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7722291	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821736	0.93[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821738	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs821739	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs821746	0.86[CEU][hapmap]
rs821749	0.86[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs890757	1.00[ASN][1000 genomes]
rs890758	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv462386	chr5:111667572-111699317	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv599372	chr5:111667572-111699317	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv437471	chr5:111682654-111691924	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17271934	SNORA13	cis	parietal	SCAN
rs17271934	EPB41L4A	cis	parietal	SCAN
rs17271934	PJA2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111675600-111687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:111676200-111689000	Weak transcription	Lung	lung
3	chr5:111678400-111689000	Weak transcription	Gastric	stomach
4	chr5:111678600-111695600	Weak transcription	Pancreas	Pancrea
5	chr5:111682600-111687800	Enhancers	Fetal Heart	heart
6	chr5:111682800-111685800	Enhancers	Right Atrium	heart
7	chr5:111683800-111689000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:111683800-111689400	Weak transcription	Spleen	Spleen
9	chr5:111684000-111702600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:111684600-111686400	Enhancers	Right Ventricle	heart
11	chr5:111684800-111688800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:111684800-111689000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:111684800-111689600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:111684800-111689600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:111685000-111685800	Enhancers	Left Ventricle	heart
16	chr5:111685000-111685800	Enhancers	Psoas Muscle	Psoas
17	chr5:111685000-111689000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:111685000-111689400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:111685000-111689600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:111685000-111689800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:111685200-111688800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:111685200-111689800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:111685200-111689800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:111685200-111689800	Weak transcription	Brain Anterior Caudate	brain
25	chr5:111685200-111690600	Weak transcription	GM12878-XiMat	blood
26	chr5:111685200-111707000	Weak transcription	Ovary	ovary
27	chr5:111685200-111709800	Weak transcription	Aorta	Aorta
28	chr5:111685600-111689400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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