Variant report

Variant	rs16878399
Chromosome Location	chr5:80367924-80367925
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	chr5:80359519..80361336-chr5:80366163..80368065,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10805936	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11738712	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741062	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11745040	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11749100	0.93[EUR][1000 genomes]
rs16878400	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6453538	0.81[EUR][1000 genomes]
rs72635623	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72635624	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72635625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72635626	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72635627	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72635628	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72635629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7722354	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7736964	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9763589	0.89[EUR][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	nsv965553	chr5:80360468-80369049	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80319600-80374200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:80337200-80368600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:80338200-80370600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:80338200-80376200	Weak transcription	NHLF	lung
5	chr5:80339200-80368600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:80339800-80374200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:80343200-80394400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:80344400-80368800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:80344800-80382600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:80353600-80375400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:80354200-80382400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:80356200-80370400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:80356600-80374600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:80361400-80374200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:80361400-80374600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:80361400-80374600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:80361600-80374200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:80361600-80374200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:80361600-80374600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:80363200-80374600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:80364200-80384200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:80364200-80386200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:80364600-80368800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:80364600-80382800	Weak transcription	Gastric	stomach
25	chr5:80364800-80371000	Weak transcription	Right Ventricle	heart
26	chr5:80365000-80370600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:80365200-80374600	Weak transcription	Fetal Intestine Small	intestine
28	chr5:80366200-80368600	Weak transcription	Primary T cells from cord blood	blood
29	chr5:80366200-80374600	Weak transcription	Ovary	ovary
30	chr5:80366600-80368000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:80366600-80368000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr5:80366600-80368400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:80366600-80368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:80366600-80368800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:80366600-80368800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr5:80366600-80370600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:80366800-80374400	Weak transcription	Adipose Nuclei	Adipose
38	chr5:80367000-80368600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:80367000-80368600	Weak transcription	HepG2	liver
40	chr5:80367200-80370800	Weak transcription	Fetal Lung	lung
41	chr5:80367600-80374600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:80367800-80370600	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:80367800-80371000	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links