Variant report

Variant	rs28820
Chromosome Location	chr5:80438350-80438351
allele	C/T
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]
rs153229	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs153230	0.81[ASN][1000 genomes]
rs153231	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs153232	0.81[ASN][1000 genomes]
rs153233	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs153234	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs153235	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs153236	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs153237	0.84[ASN][1000 genomes]
rs153238	0.84[ASN][1000 genomes]
rs153239	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs153240	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs153241	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs153242	0.83[ASN][1000 genomes]
rs153243	0.83[ASN][1000 genomes]
rs153244	0.83[ASN][1000 genomes]
rs168718	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17213885	0.93[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs173596	0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs190339	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs193786	0.96[ASN][1000 genomes]
rs2454870	0.83[ASN][1000 genomes]
rs248980	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248981	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248982	0.86[ASN][1000 genomes]
rs248983	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248984	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs248985	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248986	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs248987	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248988	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs248989	0.92[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs248990	0.81[CEU][hapmap]
rs248991	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs248992	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26889	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs26890	0.83[ASN][1000 genomes]
rs26891	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs26892	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs26893	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs26894	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs26895	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs26896	0.81[ASN][1000 genomes]
rs26898	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs27513	0.81[ASN][1000 genomes]
rs27558	0.83[ASN][1000 genomes]
rs27781	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs34115	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34116	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs34117	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34120	0.96[ASN][1000 genomes]
rs34121	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34122	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs382926	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs40046	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs457365	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs466044	0.80[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	nsv1025799	chr5:80436584-80485252	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80410600-80446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:80418400-80443800	Weak transcription	Brain Angular Gyrus	brain
3	chr5:80421800-80443600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:80422000-80443400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:80423000-80451400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:80423400-80443800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:80424400-80443800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:80424400-80445000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:80426400-80443800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:80429200-80443800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr5:80431600-80438800	Strong transcription	Primary T cells from cord blood	blood
12	chr5:80432800-80443800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:80434600-80442200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:80435800-80438800	Enhancers	Fetal Muscle Leg	muscle
15	chr5:80436200-80438600	Enhancers	Brain Hippocampus Middle	brain
16	chr5:80436200-80438800	Enhancers	Fetal Stomach	stomach
17	chr5:80436200-80442800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:80436600-80443400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr5:80436800-80438400	Enhancers	Fetal Heart	heart
20	chr5:80436800-80438600	Enhancers	Fetal Lung	lung
21	chr5:80436800-80440600	Weak transcription	Psoas Muscle	Psoas
22	chr5:80436800-80441200	Weak transcription	HepG2	liver
23	chr5:80436800-80441400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:80436800-80448600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:80437200-80440600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:80437200-80443800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:80437400-80447000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:80437600-80438600	Weak transcription	Adipose Nuclei	Adipose
29	chr5:80438000-80440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:80438200-80438400	Enhancers	Brain Anterior Caudate	brain
31	chr5:80438200-80443400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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