Variant report

Variant	rs28578275
Chromosome Location	chr5:112097234-112097235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10051624	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10071425	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10072068	0.84[EUR][1000 genomes]
rs10073398	0.85[EUR][1000 genomes]
rs10075281	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10075323	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10075377	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10076641	0.81[EUR][1000 genomes]
rs10213844	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10477483	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11241182	0.81[EUR][1000 genomes]
rs11241183	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241184	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11241185	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11749701	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11954856	0.86[EUR][1000 genomes]
rs12332692	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12513787	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12518091	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12658609	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12659119	0.86[EUR][1000 genomes]
rs13156251	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1441367	0.83[EUR][1000 genomes]
rs1465910	0.81[EUR][1000 genomes]
rs1530256	0.84[EUR][1000 genomes]
rs17285505	0.83[EUR][1000 genomes]
rs1816769	0.84[EUR][1000 genomes]
rs1866924	0.84[EUR][1000 genomes]
rs1914	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968557	0.84[EUR][1000 genomes]
rs1974786	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2019720	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2020383	0.84[EUR][1000 genomes]
rs2099810	0.85[EUR][1000 genomes]
rs2229992	0.80[ASN][1000 genomes]
rs2251913	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2253987	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2289484	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431239	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431241	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2431242	0.84[EUR][1000 genomes]
rs2431512	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431514	0.84[AMR][1000 genomes]
rs2439589	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464803	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2545158	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2546106	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2546107	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2546108	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546117	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707763	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2707765	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28373740	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2901844	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35130225	0.84[EUR][1000 genomes]
rs351772	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35414976	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390092	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs396321	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4099181	0.86[EUR][1000 genomes]
rs41116	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs414098	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs448475	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs458906	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467033	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705486	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705559	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4705573	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4705608	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4705609	0.82[EUR][1000 genomes]
rs4705610	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4705624	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511906	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs518013	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs548710	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62364017	0.88[EUR][1000 genomes]
rs6594646	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6862050	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6864688	0.87[EUR][1000 genomes]
rs6867243	0.86[EUR][1000 genomes]
rs6879057	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6894351	0.81[EUR][1000 genomes]
rs7704618	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7727738	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs861674	0.82[EUR][1000 genomes]
rs9326862	0.84[EUR][1000 genomes]
rs9326863	0.87[EUR][1000 genomes]
rs9647582	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9647583	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074400-112102800	Weak transcription	Fetal Stomach	stomach
2	chr5:112074400-112103400	Weak transcription	Left Ventricle	heart
3	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:112074600-112103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:112074800-112097600	Weak transcription	HMEC	breast
8	chr5:112075200-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:112075400-112097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:112075400-112101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
13	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:112084400-112103000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:112084600-112103200	Weak transcription	Psoas Muscle	Psoas
16	chr5:112084800-112101000	Weak transcription	Pancreas	Pancrea
17	chr5:112087200-112098200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:112087600-112117600	Weak transcription	Gastric	stomach
19	chr5:112089400-112099400	Weak transcription	Fetal Intestine Large	intestine
20	chr5:112089800-112116600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:112090000-112097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:112090400-112098400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:112091200-112097800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:112092800-112097800	Weak transcription	Fetal Brain Male	brain
25	chr5:112093400-112097400	Weak transcription	Osteobl	bone
26	chr5:112093400-112097800	Weak transcription	Aorta	Aorta
27	chr5:112093400-112102800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:112093400-112103200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:112093400-112103200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:112093400-112103200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:112093400-112103400	Weak transcription	Thymus	Thymus
32	chr5:112093400-112103600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:112093400-112103800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:112093400-112103800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:112093400-112108600	Weak transcription	Brain Angular Gyrus	brain
36	chr5:112093400-112114800	Weak transcription	Brain Substantia Nigra	brain
37	chr5:112093400-112114800	Weak transcription	NHEK	skin
38	chr5:112093400-112116000	Weak transcription	HUVEC	blood vessel
39	chr5:112093400-112117400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:112093400-112128600	Weak transcription	Ovary	ovary
41	chr5:112093400-112128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr5:112093600-112103400	Weak transcription	Fetal Kidney	kidney
44	chr5:112093800-112102200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr5:112094200-112102800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr5:112094200-112128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:112094200-112128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:112094800-112101400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:112095000-112097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:112095000-112098400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links