Variant report

Variant	rs457999
Chromosome Location	chr5:75942498-75942499
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10060984	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10061060	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10062581	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10066333	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2059219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059220	1.00[CEU][hapmap]
rs2059221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2194254	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2431348	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2432183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432185	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2455233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2455236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2909887	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2910820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937412	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2937413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2937414	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs371806	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs385385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs388058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs420138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421226	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs427380	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs439170	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs456114	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs458059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs458426	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs460617	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs462315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs462322	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs463016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs466101	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs466170	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs590674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1031881	chr5:75917033-75946265	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1017025	chr5:75926278-75946265	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
2	chr5:75903800-75943600	Weak transcription	Spleen	Spleen
3	chr5:75914200-75953800	Weak transcription	Colonic Mucosa	Colon
4	chr5:75918000-75943400	Weak transcription	Fetal Intestine Small	intestine
5	chr5:75918200-75943600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:75919200-75943600	Weak transcription	Fetal Intestine Large	intestine
7	chr5:75919200-75955400	Weak transcription	Fetal Kidney	kidney
8	chr5:75919400-75944200	Weak transcription	Fetal Lung	lung
9	chr5:75923000-75944400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr5:75924200-75943600	Weak transcription	Ovary	ovary
11	chr5:75926200-75943800	Strong transcription	Primary T cells from cord blood	blood
12	chr5:75929400-75943800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:75929800-75943800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:75929800-75945400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:75930400-75944400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:75931400-75943800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:75931600-75943600	Weak transcription	Lung	lung
18	chr5:75932200-75945400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:75934400-75943400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:75934400-75945000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:75934800-75943600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:75934800-75944600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:75935000-75943400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:75935000-75943400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:75935000-75943600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr5:75935000-75943600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr5:75935000-75943600	Strong transcription	Liver	Liver
28	chr5:75935000-75943600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:75935000-75943600	Weak transcription	Small Intestine	intestine
30	chr5:75935000-75945000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:75935000-75945400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:75935200-75945000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:75935400-75943600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr5:75935600-75943200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:75936200-75944000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:75937000-75944200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:75937200-75943600	Weak transcription	Fetal Stomach	stomach
38	chr5:75937600-75943000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:75938400-75943600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:75938600-75943600	Weak transcription	GM12878-XiMat	blood
41	chr5:75938800-75943400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:75938800-75943400	Weak transcription	Pancreas	Pancrea
43	chr5:75938800-75943400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:75938800-75943600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:75938800-75943600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:75938800-75943600	Weak transcription	Gastric	stomach
47	chr5:75938800-75943600	Weak transcription	Osteobl	bone
48	chr5:75938800-75944000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:75938800-75945400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:75939000-75943600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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