Variant report

Variant	rs6874274
Chromosome Location	chr5:80853279-80853280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10075648	0.82[CHD][hapmap]
rs10942267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10942269	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10942270	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942275	0.94[CEU][hapmap];0.82[MEX][hapmap]
rs11740689	0.94[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11743304	0.83[CEU][hapmap];0.91[MEX][hapmap]
rs11747277	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11749863	0.83[CEU][hapmap]
rs11954000	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11954508	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12515751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12521151	0.82[CEU][hapmap]
rs12521909	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173845	0.83[CEU][hapmap];0.90[MEX][hapmap]
rs13182474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13436668	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs1541830	0.82[CHD][hapmap]
rs2060584	0.91[MEX][hapmap]
rs2162973	0.85[CHD][hapmap]
rs2972230	0.86[CHD][hapmap]
rs2972245	0.85[JPT][hapmap]
rs2973341	0.86[JPT][hapmap]
rs2973343	0.86[CHD][hapmap]
rs2973350	0.86[JPT][hapmap]
rs35438373	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35586490	0.97[ASN][1000 genomes]
rs4274955	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4283765	0.89[ASN][1000 genomes]
rs4334855	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392600	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4426897	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4513668	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4529168	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599515	1.00[ASN][1000 genomes]
rs4626317	0.89[ASN][1000 genomes]
rs56005129	0.85[AFR][1000 genomes]
rs62368675	0.96[ASN][1000 genomes]
rs6452419	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs66969660	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6859225	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6866155	0.85[ASN][1000 genomes]
rs6867426	0.85[ASN][1000 genomes]
rs6868422	0.82[CHD][hapmap]
rs6868748	0.82[CHD][hapmap]
rs6869288	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6871860	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6874029	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6877102	0.85[CHD][hapmap]
rs6878037	0.86[CHD][hapmap]
rs6880200	0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs6883488	0.82[CHD][hapmap]
rs6884862	0.83[ASN][1000 genomes]
rs6887194	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887937	0.82[CHD][hapmap]
rs6890850	0.85[ASN][1000 genomes]
rs6891181	0.85[ASN][1000 genomes]
rs6895882	0.89[ASN][1000 genomes]
rs6896235	0.89[ASN][1000 genomes]
rs7702047	0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7709916	0.94[ASW][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs7711576	0.91[MEX][hapmap]
rs7717663	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7719373	0.82[CHD][hapmap]
rs7720123	0.88[ASN][1000 genomes]
rs7720445	0.83[CEU][hapmap]
rs7720736	0.84[ASN][1000 genomes]
rs7721321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7725320	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7735215	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964102	0.93[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv525225	chr5:80849084-80883110	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv2763467	chr5:80852616-80872981	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6874274	LOC644936	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
2	chr5:80825200-80865200	Weak transcription	Fetal Brain Male	brain
3	chr5:80828800-80863400	Weak transcription	Fetal Lung	lung
4	chr5:80830000-80853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:80834400-80867000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:80834800-80866400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:80834800-80870000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:80835200-80863000	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
10	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr5:80840800-80883400	Weak transcription	HSMM	muscle
13	chr5:80840800-80884600	Weak transcription	Ovary	ovary
14	chr5:80844200-80884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:80845800-80862000	Weak transcription	Thymus	Thymus
16	chr5:80845800-80863000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:80846200-80880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:80846600-80860000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:80848000-80856400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:80849000-80885600	Weak transcription	Left Ventricle	heart
21	chr5:80849400-80856200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:80850000-80860000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:80850000-80862000	Weak transcription	Primary B cells from cord blood	blood
24	chr5:80850200-80862000	Weak transcription	Primary T cells from cord blood	blood
25	chr5:80850800-80864000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:80850800-80866800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:80851400-80853400	Weak transcription	Dnd41	blood
28	chr5:80851400-80853800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:80851400-80853800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:80852200-80854200	Strong transcription	Primary hematopoietic stem cells	blood
31	chr5:80852800-80853400	Enhancers	GM12878-XiMat	blood
32	chr5:80852800-80854200	Strong transcription	Fetal Thymus	thymus

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