Variant report

Variant	rs10942268
Chromosome Location	chr5:80842234-80842235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10036942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10050981	0.90[ASN][1000 genomes]
rs10054360	1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs10056236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10057707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10060208	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10064862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069094	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs10474032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474035	1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs10514221	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12515751	0.95[YRI][hapmap]
rs13354281	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13357855	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876417	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs16898989	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28465130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28546170	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4529168	0.91[YRI][hapmap]
rs57587453	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs58238009	0.83[AFR][1000 genomes]
rs58652756	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61561045	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6452417	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6859225	0.90[YRI][hapmap]
rs6869839	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6884379	0.90[ASN][1000 genomes]
rs6887061	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6888401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893886	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6896772	1.00[JPT][hapmap]
rs6897373	1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs6898968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73133677	0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73133692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135608	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73135614	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135635	0.85[AFR][1000 genomes]
rs7717767	1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7721321	1.00[YRI][hapmap]
rs9293277	1.00[ASW][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9641	1.00[JPT][hapmap]
rs9986216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv462221	chr5:80834138-80883110	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv598751	chr5:80834138-80883110	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10942268	GALNT9	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
2	chr5:80820200-80851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80821800-80849000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
5	chr5:80827000-80848200	Weak transcription	Left Ventricle	heart
6	chr5:80828800-80863400	Weak transcription	Fetal Lung	lung
7	chr5:80830000-80848800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:80830000-80853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:80830200-80848600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:80830400-80845000	Weak transcription	Fetal Heart	heart
11	chr5:80830800-80849600	Weak transcription	Adipose Nuclei	Adipose
12	chr5:80830800-80850000	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:80831000-80845200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:80834000-80849600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:80834000-80851600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:80834400-80867000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:80834800-80866400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:80835000-80852000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:80835200-80846400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:80835200-80850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:80835200-80863000	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
24	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:80835400-80844800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:80835600-80843000	Weak transcription	Primary T cells from cord blood	blood
27	chr5:80835600-80843200	Weak transcription	Thymus	Thymus
28	chr5:80835600-80846800	Strong transcription	Fetal Thymus	thymus
29	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:80838600-80843000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:80839400-80842800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:80839400-80843200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:80839400-80845000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:80840800-80843000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:80840800-80843200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:80840800-80883400	Weak transcription	HSMM	muscle
37	chr5:80840800-80884600	Weak transcription	Ovary	ovary
38	chr5:80841000-80843200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:80841000-80843600	Weak transcription	Primary B cells from cord blood	blood
40	chr5:80841000-80848600	Weak transcription	HMEC	breast
41	chr5:80841000-80849000	Weak transcription	K562	blood
42	chr5:80841400-80842400	Enhancers	Stomach Mucosa	stomach
43	chr5:80841600-80849000	Strong transcription	Dnd41	blood
44	chr5:80841600-80849200	Weak transcription	Brain Anterior Caudate	brain
45	chr5:80841800-80843200	Weak transcription	Fetal Stomach	stomach
46	chr5:80842200-80843200	Weak transcription	Primary hematopoietic stem cells	blood

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