Variant report

Variant	rs4529168
Chromosome Location	chr5:80870584-80870585
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	chr5:80859809..80862860-chr5:80870280..80872948,3	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10054360	0.86[YRI][hapmap]
rs10056236	0.91[YRI][hapmap]
rs10057707	0.86[YRI][hapmap]
rs10064862	0.91[YRI][hapmap]
rs10066110	0.81[YRI][hapmap]
rs10069094	0.82[YRI][hapmap]
rs10075648	0.85[CHD][hapmap]
rs10474032	0.95[YRI][hapmap]
rs10474033	0.82[YRI][hapmap]
rs10474035	0.82[YRI][hapmap]
rs10514221	0.86[YRI][hapmap]
rs10942267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10942268	0.91[YRI][hapmap]
rs10942269	0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs10942270	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942274	0.81[CEU][hapmap]
rs10942275	0.88[CEU][hapmap]
rs11740689	0.90[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs11747277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11954000	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11954508	0.96[ASN][1000 genomes]
rs12153000	0.80[CHD][hapmap]
rs12515751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12521909	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13170372	0.82[CEU][hapmap]
rs13182474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1541830	0.85[CHD][hapmap]
rs16876417	0.86[YRI][hapmap]
rs16898989	0.86[YRI][hapmap]
rs2060584	0.82[CEU][hapmap]
rs2162973	0.81[CHD][hapmap]
rs2972230	0.89[CHD][hapmap]
rs2972245	0.85[JPT][hapmap]
rs2973341	0.86[JPT][hapmap]
rs2973343	0.89[CHD][hapmap]
rs2973350	0.86[JPT][hapmap]
rs35438373	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35586490	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4274955	0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4283765	0.89[ASN][1000 genomes]
rs4334855	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392600	0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][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];0.96[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs4599515	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4626317	0.89[ASN][1000 genomes]
rs62368675	0.96[ASN][1000 genomes]
rs6452414	0.80[CHD][hapmap]
rs6452419	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs66969660	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6859225	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6866155	0.85[ASN][1000 genomes]
rs6867426	0.85[ASN][1000 genomes]
rs6868422	0.85[CHD][hapmap]
rs6868748	0.85[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];0.96[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6874274	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]
rs6877102	0.81[CHD][hapmap]
rs6878037	0.89[CHD][hapmap]
rs6880200	0.91[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs6883488	0.85[CHD][hapmap]
rs6884862	0.83[ASN][1000 genomes]
rs6887061	0.90[YRI][hapmap]
rs6887194	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6887937	0.85[CHD][hapmap]
rs6888401	0.90[YRI][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]
rs6897373	0.82[YRI][hapmap]
rs6898968	0.91[YRI][hapmap]
rs7702047	0.81[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7711020	0.81[CHD][hapmap]
rs7711576	0.82[CEU][hapmap]
rs7717663	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7719373	0.85[CHD][hapmap]
rs7720123	0.88[ASN][1000 genomes]
rs7720736	0.84[ASN][1000 genomes]
rs7721321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7725320	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7735215	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293275	0.80[CHD][hapmap]
rs9293277	0.86[YRI][hapmap]
rs964102	0.89[CHD][hapmap]
rs9986216	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv2763467	chr5:80852616-80872981	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4529168	TBCA	cis	cerebellum	SCAN
rs4529168	LOC644936	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80803600-80875200	Weak transcription	Fetal Brain Female	brain
2	chr5:80835200-80872800	Weak transcription	Fetal Kidney	kidney
3	chr5:80835200-80875200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:80835600-80876000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr5:80840800-80883400	Weak transcription	HSMM	muscle
6	chr5:80840800-80884600	Weak transcription	Ovary	ovary
7	chr5:80844200-80884600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:80846200-80880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:80849000-80885600	Weak transcription	Left Ventricle	heart
10	chr5:80860200-80878800	Weak transcription	Esophagus	oesophagus
11	chr5:80862400-80874800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:80862800-80878800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:80863800-80872000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:80864200-80886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:80864200-80894200	Weak transcription	Fetal Lung	lung
16	chr5:80864600-80894200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:80864800-80875200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:80865000-80871600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:80865000-80875200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:80867800-80870600	Strong transcription	Fetal Thymus	thymus
21	chr5:80867800-80875200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr5:80868200-80871200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:80868600-80875200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:80868800-80871000	Weak transcription	HUVEC	blood vessel
25	chr5:80869200-80875400	Weak transcription	Primary T cells from cord blood	blood
26	chr5:80869400-80871800	Strong transcription	Dnd41	blood
27	chr5:80869400-80887600	Weak transcription	Fetal Stomach	stomach
28	chr5:80869800-80870800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:80869800-80870800	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr5:80869800-80886400	Weak transcription	Thymus	Thymus
31	chr5:80870000-80870600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr5:80870000-80871000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:80870000-80887600	Weak transcription	Aorta	Aorta
34	chr5:80870200-80875200	Weak transcription	GM12878-XiMat	blood
35	chr5:80870400-80870600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr5:80870400-80870600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:80870400-80870600	ZNF genes & repeats	Colon Smooth Muscle	Colon

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