Variant report

Variant	rs153239
Chromosome Location	chr5:80425860-80425861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12659839	0.90[JPT][hapmap]
rs153229	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs153230	0.94[ASN][1000 genomes]
rs153231	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153232	0.94[ASN][1000 genomes]
rs153233	0.86[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153234	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153235	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153236	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153237	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153238	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153242	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153243	0.97[ASN][1000 genomes]
rs153244	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168718	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs17213885	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs173596	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs190339	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193786	0.90[ASN][1000 genomes]
rs2454870	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248980	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248981	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248982	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248983	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs248984	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248985	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248986	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248987	0.87[ASN][1000 genomes]
rs248988	0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248989	0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248992	0.89[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs26889	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26890	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26891	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs26892	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs26893	0.81[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs26894	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs26895	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs26896	0.94[ASN][1000 genomes]
rs26898	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs27513	0.94[ASN][1000 genomes]
rs27558	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27781	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28820	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs34115	0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs34116	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs34117	0.89[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs34120	0.90[ASN][1000 genomes]
rs34121	0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs34122	0.89[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs382926	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40046	0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs457365	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs466044	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58200570	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv882232	chr5:80393949-80436584	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80404800-80428200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:80407000-80428000	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:80408800-80426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:80410600-80432400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:80410600-80446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:80411200-80427800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:80414200-80438000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:80417800-80427200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:80417800-80428800	Weak transcription	Right Atrium	heart
10	chr5:80417800-80436200	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:80418400-80443800	Weak transcription	Brain Angular Gyrus	brain
12	chr5:80419200-80429200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr5:80419400-80438200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:80421200-80435800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:80421800-80443600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:80422000-80427200	Weak transcription	Brain Anterior Caudate	brain
17	chr5:80422000-80429000	Weak transcription	Brain Substantia Nigra	brain
18	chr5:80422000-80436200	Weak transcription	Adipose Nuclei	Adipose
19	chr5:80422000-80443400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:80422200-80436200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:80422400-80436200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:80423000-80427200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:80423000-80451400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:80423400-80436200	Weak transcription	Ovary	ovary
25	chr5:80423400-80436400	Weak transcription	Left Ventricle	heart
26	chr5:80423400-80443800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:80424200-80426000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:80424200-80433800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:80424400-80434400	Weak transcription	HepG2	liver
30	chr5:80424400-80443800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr5:80424400-80445000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:80425200-80426000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:80425200-80426800	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:80425200-80428400	Strong transcription	Primary T cells from cord blood	blood
35	chr5:80425600-80426800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:80425600-80428000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:80425600-80428400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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