Variant report

Variant	rs62342558
Chromosome Location	chr5:7908193-7908194
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10066017	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512930	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520873	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12186809	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16879418	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879420	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267793	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776457	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776465	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797191	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55872008	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57240487	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57989551	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59253244	0.83[EUR][1000 genomes]
rs62342528	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62342552	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62345660	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67514505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67902045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703033	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv508345	chr5:7890892-7933471	Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62342558	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:7895400-7909600	Weak transcription	Fetal Heart	heart
4	chr5:7899600-7910000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:7899600-7912000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:7899800-7909200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:7899800-7909200	Weak transcription	Esophagus	oesophagus
8	chr5:7900000-7909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:7900000-7914600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:7900600-7909200	Weak transcription	Gastric	stomach
11	chr5:7902200-7909000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:7902400-7909000	Weak transcription	Aorta	Aorta
13	chr5:7902400-7909000	Weak transcription	Right Ventricle	heart
14	chr5:7902400-7909000	Weak transcription	K562	blood
15	chr5:7902400-7910200	Weak transcription	Fetal Brain Male	brain
16	chr5:7902400-7910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:7902400-7911200	Weak transcription	Fetal Kidney	kidney
18	chr5:7902800-7911200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:7903400-7908200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:7903400-7908200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:7903400-7909000	Weak transcription	Colonic Mucosa	Colon
22	chr5:7903400-7909200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:7903400-7911000	Weak transcription	Fetal Thymus	thymus
24	chr5:7903600-7908200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:7903600-7909000	Weak transcription	Brain Angular Gyrus	brain
26	chr5:7903600-7909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:7903600-7916000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:7903800-7913600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:7904000-7908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:7904000-7909000	Weak transcription	Lung	lung
31	chr5:7904000-7909000	Weak transcription	Spleen	Spleen
32	chr5:7904000-7911400	Weak transcription	Small Intestine	intestine
33	chr5:7904200-7909000	Weak transcription	Placenta	Placenta
34	chr5:7904200-7909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:7904200-7909800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:7904200-7910800	Weak transcription	Thymus	Thymus
37	chr5:7904200-7912000	Weak transcription	Pancreas	Pancrea
38	chr5:7904200-7912200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:7904400-7908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:7904400-7909000	Weak transcription	Brain Germinal Matrix	brain
41	chr5:7904400-7909000	Weak transcription	Left Ventricle	heart
42	chr5:7904400-7909200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:7904400-7909800	Weak transcription	Hela-S3	cervix
44	chr5:7904400-7911000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:7904400-7912400	Weak transcription	HMEC	breast
46	chr5:7904400-7915800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:7904600-7909600	Strong transcription	A549	lung
48	chr5:7904800-7915400	Weak transcription	Osteobl	bone
49	chr5:7905000-7908800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:7905000-7909000	Weak transcription	Brain Inferior Temporal Lobe	brain

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