Variant report

Variant	rs1423380
Chromosome Location	chr5:100221189-100221190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10043056	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10044903	0.82[EUR][1000 genomes]
rs10052474	0.82[EUR][1000 genomes]
rs10058901	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059470	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10059846	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069305	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10075853	0.83[TSI][hapmap]
rs10078934	0.83[EUR][1000 genomes]
rs10214216	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10463771	0.83[EUR][1000 genomes]
rs10463772	0.83[EUR][1000 genomes]
rs10477661	0.89[EUR][1000 genomes]
rs10478599	0.83[TSI][hapmap]
rs10478633	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10478649	0.89[EUR][1000 genomes]
rs11241752	0.92[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs11241755	0.92[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs11584	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11738152	0.83[EUR][1000 genomes]
rs11742480	0.83[EUR][1000 genomes]
rs11742504	0.83[EUR][1000 genomes]
rs12153670	0.80[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13355889	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13358325	0.80[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1423384	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423385	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428439	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1541676	0.89[GIH][hapmap];0.83[EUR][1000 genomes]
rs1559058	0.83[EUR][1000 genomes]
rs1559059	0.82[EUR][1000 genomes]
rs17723545	0.83[EUR][1000 genomes]
rs17724185	0.82[EUR][1000 genomes]
rs17725452	0.84[EUR][1000 genomes]
rs17725678	0.83[EUR][1000 genomes]
rs17726244	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17780091	0.81[EUR][1000 genomes]
rs17780273	0.81[EUR][1000 genomes]
rs17780471	0.81[EUR][1000 genomes]
rs17780525	0.83[EUR][1000 genomes]
rs17782041	0.83[EUR][1000 genomes]
rs17782250	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1820150	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1833862	0.86[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2059845	0.82[EUR][1000 genomes]
rs2059846	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2400313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544913	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544920	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2548256	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2548257	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548263	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2548276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548278	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548279	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548280	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2725116	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725124	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28413976	0.81[EUR][1000 genomes]
rs3756350	0.82[EUR][1000 genomes]
rs3756351	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756352	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756353	0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756354	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3756355	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776167	0.80[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs3776168	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776171	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776174	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822366	0.82[EUR][1000 genomes]
rs3846627	0.82[EUR][1000 genomes]
rs3857365	0.82[EUR][1000 genomes]
rs3909452	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs4702991	0.82[EUR][1000 genomes]
rs4703126	0.81[EUR][1000 genomes]
rs4703127	0.83[EUR][1000 genomes]
rs4703128	0.81[EUR][1000 genomes]
rs4703130	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4703131	0.90[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs4703133	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55849330	0.80[EUR][1000 genomes]
rs55959219	0.83[EUR][1000 genomes]
rs59030588	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59490571	0.83[EUR][1000 genomes]
rs60663279	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60853907	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726971	0.81[EUR][1000 genomes]
rs72778607	0.82[EUR][1000 genomes]
rs72778613	0.81[EUR][1000 genomes]
rs72778620	0.81[EUR][1000 genomes]
rs72778635	0.85[EUR][1000 genomes]
rs7447673	0.83[EUR][1000 genomes]
rs7703643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7737721	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327319	0.83[EUR][1000 genomes]
rs9327323	0.83[EUR][1000 genomes]
rs9327327	0.83[EUR][1000 genomes]
rs966257	0.83[EUR][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
rs1423380	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100191200-100224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:100191200-100225200	Weak transcription	Fetal Lung	lung
3	chr5:100200200-100234400	Weak transcription	Fetal Brain Male	brain
4	chr5:100207600-100225000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:100208000-100235800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:100208800-100223600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:100209600-100225600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:100210200-100222600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:100210400-100223800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:100213200-100223400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr5:100213800-100223600	Weak transcription	Spleen	Spleen
12	chr5:100214000-100224400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr5:100214800-100222200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:100215400-100224000	Weak transcription	Colonic Mucosa	Colon
15	chr5:100215600-100222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:100217000-100225000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:100217400-100224400	ZNF genes & repeats	GM12878-XiMat	blood
18	chr5:100218400-100222400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:100218800-100222200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:100218800-100223200	Strong transcription	Fetal Thymus	thymus
21	chr5:100218800-100223800	Weak transcription	Fetal Brain Female	brain
22	chr5:100218800-100224200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr5:100218800-100225000	Weak transcription	Adipose Nuclei	Adipose
24	chr5:100218800-100225800	Weak transcription	Placenta	Placenta
25	chr5:100219000-100221800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:100219000-100233400	Weak transcription	Brain Germinal Matrix	brain
27	chr5:100219200-100226200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:100219600-100225000	Weak transcription	Thymus	Thymus
29	chr5:100220200-100224600	Genic enhancers	Dnd41	blood
30	chr5:100220400-100221800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:100220400-100224600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:100220600-100221600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr5:100220600-100224000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:100220800-100221600	Weak transcription	Primary B cells from cord blood	blood
35	chr5:100220800-100222400	Weak transcription	Primary T cells from cord blood	blood
36	chr5:100220800-100223000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr5:100220800-100223000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:100220800-100223600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:100220800-100224200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:100220800-100224800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:100220800-100225400	Weak transcription	HUVEC	blood vessel
42	chr5:100221000-100221800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:100221000-100221800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:100221000-100221800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr5:100221000-100222000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:100221000-100222200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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