Variant report

Variant	rs1428439
Chromosome Location	chr5:100238801-100238802
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	chr15:75932135..75932772-chr5:100238542..100239334,2	NB4	blood:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10035529	0.82[AMR][1000 genomes]
rs10043056	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10044903	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10052474	0.85[EUR][1000 genomes]
rs10058901	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10059470	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10059846	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069305	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075853	0.83[TSI][hapmap]
rs10078934	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10214216	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10463771	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10463772	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10477661	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10478599	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs10478633	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10478649	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10515303	0.81[EUR][1000 genomes]
rs11241752	0.85[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11241755	0.85[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs11584	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11738152	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11742480	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11742504	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12153670	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13354021	0.83[AMR][1000 genomes]
rs13355889	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358325	0.81[CEU][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1423380	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]
rs1423384	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1423385	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1541676	0.85[CEU][hapmap];0.94[GIH][hapmap];0.86[EUR][1000 genomes]
rs1559058	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1559059	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17723545	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17724185	0.85[EUR][1000 genomes]
rs17725452	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17725678	0.87[EUR][1000 genomes]
rs17726244	0.88[EUR][1000 genomes]
rs17780091	0.84[EUR][1000 genomes]
rs17780273	0.84[EUR][1000 genomes]
rs17780471	0.84[EUR][1000 genomes]
rs17780525	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17782041	0.87[EUR][1000 genomes]
rs17782250	0.88[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1820150	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1833862	0.81[CEU][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2059845	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2059846	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2400313	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2544913	0.87[CEU][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544920	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2548256	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548257	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548263	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2548276	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548278	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548279	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548280	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2725116	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2725124	0.93[CHB][hapmap];0.88[CHD][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28413976	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34564041	0.81[EUR][1000 genomes]
rs3756350	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs3756351	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756352	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756353	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756354	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756355	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776167	0.85[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3776168	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776170	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776174	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776176	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822366	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs3846627	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3857365	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3909452	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs4702991	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4703126	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4703127	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4703128	0.84[EUR][1000 genomes]
rs4703130	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703131	0.85[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs4703133	0.89[EUR][1000 genomes]
rs55849330	0.83[EUR][1000 genomes]
rs55861847	0.81[EUR][1000 genomes]
rs55959219	0.87[EUR][1000 genomes]
rs56752243	0.81[EUR][1000 genomes]
rs59030588	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59490571	0.86[EUR][1000 genomes]
rs60663279	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60853907	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726971	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs72778607	0.85[EUR][1000 genomes]
rs72778613	0.84[EUR][1000 genomes]
rs72778620	0.84[EUR][1000 genomes]
rs72778635	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7447673	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7703643	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7737721	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9327319	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9327323	0.86[EUR][1000 genomes]
rs9327327	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs966257	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv882471	chr5:100234439-100362071	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv882472	chr5:100234439-100512338	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1428439	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100232600-100245600	Active TSS	GM12878-XiMat	blood
2	chr5:100235400-100241400	Active TSS	Duodenum Mucosa	Duodenum
3	chr5:100235600-100239000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:100235600-100240400	Active TSS	Brain Angular Gyrus	brain
5	chr5:100235600-100240600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:100235600-100240600	Active TSS	Thymus	Thymus
7	chr5:100235800-100239600	Active TSS	HSMMtube	muscle
8	chr5:100235800-100239800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:100235800-100240400	Active TSS	Brain Anterior Caudate	brain
10	chr5:100235800-100240400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:100235800-100240400	Active TSS	Lung	lung
12	chr5:100235800-100240600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
13	chr5:100235800-100240600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr5:100235800-100241000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:100235800-100241400	Active TSS	Right Atrium	heart
16	chr5:100236000-100239000	Active TSS	Colon Smooth Muscle	Colon
17	chr5:100236000-100239400	Active TSS	Primary T cells from cord blood	blood
18	chr5:100236000-100239600	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr5:100236000-100239600	Active TSS	A549	lung
20	chr5:100236000-100239800	Active TSS	NHDF-Ad	bronchial
21	chr5:100236000-100240400	Active TSS	Colonic Mucosa	Colon
22	chr5:100236000-100240400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
23	chr5:100236000-100240400	Active TSS	Small Intestine	intestine
24	chr5:100236000-100240600	Active TSS	Right Ventricle	heart
25	chr5:100236000-100240600	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr5:100236000-100240800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:100236200-100239200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:100236200-100239200	Active TSS	Fetal Brain Male	brain
29	chr5:100236200-100239200	Active TSS	Gastric	stomach
30	chr5:100236200-100239400	Active TSS	Primary monocytes fromperipheralblood	blood
31	chr5:100236200-100239600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:100236200-100239600	Active TSS	Fetal Lung	lung
33	chr5:100236200-100240800	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr5:100236200-100241200	Active TSS	Liver	Liver
35	chr5:100236200-100241400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr5:100236400-100239200	Active TSS	Fetal Thymus	thymus
37	chr5:100236400-100239200	Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:100236400-100239400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:100236600-100240800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:100237000-100239600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr5:100237000-100240400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
42	chr5:100237200-100239200	Active TSS	Osteobl	bone
43	chr5:100237200-100239400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
44	chr5:100237200-100239600	Active TSS	Primary B cells from peripheral blood	blood
45	chr5:100237200-100239600	Active TSS	Placenta	Placenta
46	chr5:100237200-100239800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr5:100237200-100239800	Active TSS	Placenta Amnion	Placenta Amnion
48	chr5:100237200-100240000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr5:100237200-100240200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:100237200-100240400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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