Variant report

Variant	rs2896839
Chromosome Location	chr5:118540291-118540292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10035593	0.93[EUR][1000 genomes]
rs10037918	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10051559	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10072072	1.00[CEU][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs10075997	0.90[EUR][1000 genomes]
rs11241487	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1394628	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1504974	0.83[EUR][1000 genomes]
rs1504975	1.00[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1504976	1.00[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1553542	0.82[EUR][1000 genomes]
rs1857771	0.83[EUR][1000 genomes]
rs1910788	0.95[EUR][1000 genomes]
rs2271059	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2404397	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2896840	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs3797337	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3992620	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6880106	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs73242994	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73242996	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7736744	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9327092	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1019788	chr5:118488501-118607405	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv537882	chr5:118488501-118607405	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1034616	chr5:118506348-118600391	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1031914	chr5:118516878-118589497	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118483000-118541400	Weak transcription	NHEK	skin
2	chr5:118485800-118572200	Weak transcription	Small Intestine	intestine
3	chr5:118486000-118588600	Weak transcription	Right Ventricle	heart
4	chr5:118489800-118591200	Weak transcription	Colonic Mucosa	Colon
5	chr5:118498000-118584200	Weak transcription	Spleen	Spleen
6	chr5:118503800-118585800	Weak transcription	NH-A	brain
7	chr5:118505400-118554600	Weak transcription	HepG2	liver
8	chr5:118507800-118580200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:118514400-118589000	Weak transcription	Pancreas	Pancrea
10	chr5:118514400-118591400	Weak transcription	Esophagus	oesophagus
11	chr5:118514600-118554800	Weak transcription	NHDF-Ad	bronchial
12	chr5:118516000-118544000	Weak transcription	Hela-S3	cervix
13	chr5:118516200-118554800	Weak transcription	Osteobl	bone
14	chr5:118521200-118571000	Weak transcription	HMEC	breast
15	chr5:118524200-118570800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:118524400-118571000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:118524600-118561200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:118524600-118584200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:118525400-118541000	Strong transcription	Liver	Liver
20	chr5:118527800-118549000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:118532200-118540800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr5:118532800-118540600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:118534600-118574200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:118534800-118542000	Weak transcription	A549	lung
25	chr5:118535000-118544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:118535000-118554600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:118535000-118560800	Weak transcription	Gastric	stomach
28	chr5:118535000-118579600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:118535000-118584800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:118535000-118587400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:118535000-118588200	Weak transcription	Lung	lung
32	chr5:118535000-118589000	Weak transcription	Aorta	Aorta
33	chr5:118535200-118542000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:118535200-118544000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:118535200-118548000	Weak transcription	Fetal Heart	heart
36	chr5:118535200-118548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:118535200-118548200	Weak transcription	HSMMtube	muscle
38	chr5:118535200-118555600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:118535200-118575200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:118535400-118553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:118535400-118554600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:118535400-118555400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:118535400-118569400	Weak transcription	Thymus	Thymus
44	chr5:118535600-118548600	Weak transcription	Psoas Muscle	Psoas
45	chr5:118535600-118554800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:118535600-118555800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:118535800-118554400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr5:118536000-118554600	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:118536400-118556000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:118536400-118556200	Weak transcription	Stomach Smooth Muscle	stomach

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