Variant report

Variant	rs17725452
Chromosome Location	chr5:100229953-100229954
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:100229842-100229979	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:100229581-100229956	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ST8SIA4	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10043056	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10044903	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10052474	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10057237	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10058901	0.84[EUR][1000 genomes]
rs10059470	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10059846	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10069305	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10075853	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078251	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10078934	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10214216	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10463771	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10463772	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10477661	0.81[EUR][1000 genomes]
rs10478598	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10478599	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10478633	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10478649	0.81[EUR][1000 genomes]
rs10515303	0.92[EUR][1000 genomes]
rs11241752	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241755	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241794	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11738152	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11741369	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742480	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11742504	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748306	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12153670	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12332145	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12332642	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12719316	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13355889	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13357545	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13358325	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13436424	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13857	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423380	0.84[EUR][1000 genomes]
rs1423384	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs1423385	0.94[EUR][1000 genomes]
rs1428439	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1541676	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559058	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1559059	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17723545	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17724185	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17725678	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17726346	0.91[EUR][1000 genomes]
rs17780091	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17780273	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17780471	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17780525	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17782041	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17782250	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1820150	0.81[EUR][1000 genomes]
rs1833862	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2059845	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2059846	0.90[EUR][1000 genomes]
rs2400313	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2544920	0.83[ASN][1000 genomes]
rs2548257	0.90[EUR][1000 genomes]
rs2548263	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2548276	0.81[EUR][1000 genomes]
rs2548278	0.81[EUR][1000 genomes]
rs2548279	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs2725116	0.81[EUR][1000 genomes]
rs28413976	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34564041	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3756350	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756351	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3756352	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3756353	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3756354	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3756355	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3776155	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776167	0.90[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776168	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs3776170	0.83[EUR][1000 genomes]
rs3776171	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3776174	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3776176	0.84[EUR][1000 genomes]
rs3822366	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3843478	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3846627	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3857365	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3909452	0.81[EUR][1000 genomes]
rs3909453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4702991	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703126	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703127	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703128	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4703130	0.93[EUR][1000 genomes]
rs4703131	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55805984	0.91[EUR][1000 genomes]
rs55849330	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55861847	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55959219	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55968003	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56752243	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59030588	0.83[EUR][1000 genomes]
rs59490571	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60663279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60853907	0.85[EUR][1000 genomes]
rs726971	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72776700	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72778607	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72778613	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72778620	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72778635	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778649	0.91[EUR][1000 genomes]
rs72778650	0.90[EUR][1000 genomes]
rs7447673	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7703643	0.83[EUR][1000 genomes]
rs7737721	0.82[EUR][1000 genomes]
rs9327319	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327323	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9327327	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs966257	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17725452	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100200200-100234400	Weak transcription	Fetal Brain Male	brain
2	chr5:100208000-100235800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:100219000-100233400	Weak transcription	Brain Germinal Matrix	brain
4	chr5:100225000-100231600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:100225200-100233800	Weak transcription	Thymus	Thymus
6	chr5:100226400-100233800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:100226400-100235600	Weak transcription	Placenta	Placenta
8	chr5:100226800-100233800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:100227000-100234400	Weak transcription	Right Atrium	heart
10	chr5:100227000-100235600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:100227200-100231600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:100227200-100232800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:100227200-100232800	Weak transcription	Osteobl	bone
14	chr5:100227200-100235600	Weak transcription	Fetal Lung	lung
15	chr5:100227400-100230200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:100227400-100230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:100227600-100230000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:100227600-100231800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:100227800-100230000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:100228000-100231200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:100228000-100231400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:100228000-100231600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:100228000-100232600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr5:100228200-100231200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:100228600-100230800	Genic enhancers	Dnd41	blood
26	chr5:100228600-100231800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr5:100229000-100231000	Strong transcription	HUVEC	blood vessel
28	chr5:100229000-100231600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:100229200-100230000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr5:100229200-100232000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:100229200-100235400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:100229400-100231400	Strong transcription	Primary B cells from cord blood	blood
33	chr5:100229400-100231400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:100229400-100232400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:100229600-100230200	Genic enhancers	Primary T cells from cord blood	blood
36	chr5:100229600-100230400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:100229600-100231000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr5:100229600-100231000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:100229600-100231200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr5:100229600-100232200	Strong transcription	Fetal Thymus	thymus
41	chr5:100229800-100231200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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