Variant report

Variant	rs1541798
Chromosome Location	chr5:94806961-94806962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10053324	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10076499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1183640	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981952	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545841	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548652	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560257	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2560260	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560261	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2731826	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2731833	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2881976	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61270217	0.82[ASN][1000 genomes]
rs6556870	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73777211	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9314148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv598954	chr5:94783175-94859599	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94780400-94810800	Weak transcription	Pancreas	Pancrea
2	chr5:94782000-94810200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:94788400-94811200	Weak transcription	Small Intestine	intestine
4	chr5:94788800-94822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:94790600-94810800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:94791800-94811200	Weak transcription	Hela-S3	cervix
7	chr5:94792600-94817800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:94792600-94821800	Weak transcription	Right Ventricle	heart
9	chr5:94794400-94810800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:94794600-94810800	Weak transcription	Spleen	Spleen
11	chr5:94794800-94807400	Weak transcription	Psoas Muscle	Psoas
12	chr5:94794800-94817600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:94795200-94826600	Weak transcription	NHEK	skin
14	chr5:94795400-94810400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:94795400-94814000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:94795600-94807200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:94796000-94810800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:94796800-94810800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:94797000-94817000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:94797000-94819200	Weak transcription	HepG2	liver
21	chr5:94797200-94807200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:94797200-94811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:94797400-94810800	Weak transcription	Fetal Intestine Small	intestine
24	chr5:94799000-94807800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:94799200-94807600	Weak transcription	Aorta	Aorta
26	chr5:94799200-94810800	Weak transcription	Esophagus	oesophagus
27	chr5:94799200-94810800	Weak transcription	Fetal Stomach	stomach
28	chr5:94799200-94810800	Weak transcription	Gastric	stomach
29	chr5:94799200-94810800	Weak transcription	Lung	lung
30	chr5:94799200-94810800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:94799200-94810800	Weak transcription	Thymus	Thymus
32	chr5:94799200-94811000	Weak transcription	Ovary	ovary
33	chr5:94799200-94811200	Weak transcription	Brain Angular Gyrus	brain
34	chr5:94799200-94811200	Weak transcription	Colonic Mucosa	Colon
35	chr5:94799200-94811200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:94799200-94812200	Weak transcription	Fetal Kidney	kidney
37	chr5:94799200-94821600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:94799200-94834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:94799400-94807400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:94799400-94807600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:94801600-94808400	Strong transcription	Placenta	Placenta
42	chr5:94802000-94821600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:94802200-94810800	Weak transcription	Left Ventricle	heart
44	chr5:94802200-94813600	Weak transcription	HMEC	breast
45	chr5:94802200-94816200	Weak transcription	Fetal Brain Male	brain
46	chr5:94802400-94807000	Weak transcription	HSMMtube	muscle
47	chr5:94802400-94807200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:94802400-94808600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:94802600-94807200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:94804200-94817800	Weak transcription	Fetal Heart	heart

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