Variant report

Variant	rs17780273
Chromosome Location	chr5:100173741-100173742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10043056	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10044903	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10052474	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10057237	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10058901	0.81[EUR][1000 genomes]
rs10059470	0.82[EUR][1000 genomes]
rs10059846	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10069305	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10075853	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10078251	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10078934	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214216	0.84[EUR][1000 genomes]
rs10463771	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10463772	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478598	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478599	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478633	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10515303	0.89[EUR][1000 genomes]
rs11241752	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11241755	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11241794	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11738152	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741369	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11742480	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742504	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748306	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12153670	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332145	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12332642	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12719316	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13355889	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13357545	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13358325	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13436424	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13857	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1423380	0.81[EUR][1000 genomes]
rs1423384	0.91[EUR][1000 genomes]
rs1423385	0.91[EUR][1000 genomes]
rs1428439	0.84[EUR][1000 genomes]
rs1541676	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1559058	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559059	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17723545	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17724185	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17725452	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17725678	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17726346	0.88[EUR][1000 genomes]
rs17780091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17780471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17780525	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782041	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17782250	0.84[EUR][1000 genomes]
rs1820150	0.84[EUR][1000 genomes]
rs1833862	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2059845	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059846	0.92[EUR][1000 genomes]
rs2400313	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2544913	0.82[EUR][1000 genomes]
rs2544920	0.87[ASN][1000 genomes]
rs2548257	0.93[EUR][1000 genomes]
rs2548263	0.88[EUR][1000 genomes]
rs2548276	0.84[EUR][1000 genomes]
rs2548278	0.84[EUR][1000 genomes]
rs2548279	0.94[EUR][1000 genomes]
rs2725116	0.84[EUR][1000 genomes]
rs28413976	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34564041	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3756350	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756351	0.85[EUR][1000 genomes]
rs3756352	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3756353	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3756354	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3756355	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3776155	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776167	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776168	0.93[EUR][1000 genomes]
rs3776170	0.82[EUR][1000 genomes]
rs3776171	0.85[EUR][1000 genomes]
rs3776174	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3776176	0.81[EUR][1000 genomes]
rs3822366	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3843478	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846627	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3857365	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3909452	0.84[EUR][1000 genomes]
rs3909453	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4702991	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703127	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703128	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4703130	0.90[EUR][1000 genomes]
rs4703131	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55805984	0.88[EUR][1000 genomes]
rs55849330	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55861847	0.89[EUR][1000 genomes]
rs55959219	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55968003	0.87[EUR][1000 genomes]
rs56752243	0.89[EUR][1000 genomes]
rs59030588	0.82[EUR][1000 genomes]
rs59490571	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60663279	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60853907	0.82[EUR][1000 genomes]
rs726971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72776700	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72778607	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72778613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778620	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778635	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72778649	0.88[EUR][1000 genomes]
rs72778650	0.87[EUR][1000 genomes]
rs7447673	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703643	0.82[EUR][1000 genomes]
rs7737721	0.83[EUR][1000 genomes]
rs9327319	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9327323	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327327	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966257	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	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
3	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
rs17780273	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
3	chr5:100164000-100173800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:100164200-100174800	Weak transcription	Placenta	Placenta
5	chr5:100164200-100176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:100164400-100175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:100164400-100175800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:100164600-100174800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:100164600-100175000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:100165000-100174800	Weak transcription	Primary T cells from cord blood	blood
11	chr5:100165000-100175800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:100165000-100176200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:100165000-100176800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:100165600-100174200	ZNF genes & repeats	GM12878-XiMat	blood
15	chr5:100168800-100176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:100170400-100174200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:100170600-100179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:100170800-100173800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:100172000-100174200	Strong transcription	Primary B cells from cord blood	blood
20	chr5:100172400-100173800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr5:100172400-100176400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr5:100172600-100174000	Enhancers	Fetal Lung	lung
23	chr5:100172600-100174600	Strong transcription	Dnd41	blood
24	chr5:100173200-100173800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr5:100173200-100173800	Genic enhancers	Monocytes-CD14+_RO01746	blood
26	chr5:100173200-100174000	Enhancers	A549	lung
27	chr5:100173200-100177000	Enhancers	HUVEC	blood vessel
28	chr5:100173400-100173800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:100173400-100173800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr5:100173400-100174000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:100173400-100174200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:100173400-100174800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:100173600-100173800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:100173600-100173800	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr5:100173600-100174000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr5:100173600-100174200	Enhancers	Fetal Kidney	kidney
37	chr5:100173600-100176000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:100173600-100176600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr5:100173600-100176600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:100173600-100176800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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