Variant report

Variant	rs2973343
Chromosome Location	chr5:80836498-80836499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10036712	0.93[JPT][hapmap];0.90[YRI][hapmap]
rs10042303	0.92[JPT][hapmap];0.88[YRI][hapmap]
rs10454898	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10942269	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs11740689	0.86[CHD][hapmap]
rs12153000	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188888	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2917542	0.80[YRI][hapmap]
rs2972228	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972230	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972232	0.96[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972244	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972245	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2973341	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973347	0.84[GIH][hapmap];0.88[TSI][hapmap]
rs2973350	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34414290	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4274955	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs4392600	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs4426897	0.93[JPT][hapmap]
rs4513668	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs4529168	0.89[CHD][hapmap]
rs6452414	0.83[CHD][hapmap]
rs6452416	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6452419	0.93[JPT][hapmap]
rs6869288	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6871860	0.93[JPT][hapmap]
rs6874029	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs6874274	0.86[CHD][hapmap]
rs6878037	0.93[CHD][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6880200	1.00[JPT][hapmap]
rs7702047	0.86[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7717663	0.93[JPT][hapmap]
rs7720123	0.81[ASN][1000 genomes]
rs7720736	0.82[ASN][1000 genomes]
rs7721321	0.92[JPT][hapmap]
rs7725320	0.93[JPT][hapmap]
rs7733938	0.84[JPT][hapmap];0.86[YRI][hapmap]
rs9293275	0.83[CHD][hapmap]
rs964102	0.85[JPT][hapmap];0.83[LWK][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2973343	C19orf24	trans	parietal	SCAN
rs2973343	CTD-2249K22.1	cis	Thyroid	GTEx

Chromatin state (count:43 , 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	chr5:80821800-80836800	Weak transcription	NHDF-Ad	bronchial
4	chr5:80821800-80849000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
6	chr5:80827000-80840600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:80827000-80848200	Weak transcription	Left Ventricle	heart
8	chr5:80828800-80863400	Weak transcription	Fetal Lung	lung
9	chr5:80830000-80848800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:80830000-80853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr5:80830200-80848600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:80830400-80845000	Weak transcription	Fetal Heart	heart
13	chr5:80830600-80840200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:80830600-80841400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:80830800-80849600	Weak transcription	Adipose Nuclei	Adipose
16	chr5:80830800-80850000	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:80831000-80845200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:80833800-80841400	Weak transcription	Stomach Mucosa	stomach
19	chr5:80834000-80836600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:80834000-80849600	Weak transcription	Brain Angular Gyrus	brain
21	chr5:80834000-80851600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:80834200-80836600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:80834200-80838600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr5:80834400-80838600	Genic enhancers	Dnd41	blood
25	chr5:80834400-80840200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:80834400-80867000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:80834800-80866400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:80835000-80852000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:80835200-80837800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:80835200-80846400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:80835200-80850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:80835200-80863000	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
35	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:80835400-80844800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:80835600-80836800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:80835600-80843000	Weak transcription	Primary T cells from cord blood	blood
39	chr5:80835600-80843200	Weak transcription	Thymus	Thymus
40	chr5:80835600-80846800	Strong transcription	Fetal Thymus	thymus
41	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:80836000-80839400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr5:80836200-80836800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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