Variant report

Variant	rs4417425
Chromosome Location	chr13:95282534-95282535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95281545..95283175-chr13:95286843..95288996,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs16949940	0.82[CEU][hapmap]
rs16949977	1.00[ASN][1000 genomes]
rs2146822	1.00[ASN][1000 genomes]
rs2226077	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2226078	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516070	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59149020	1.00[ASN][1000 genomes]
rs61707735	1.00[ASN][1000 genomes]
rs61965606	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492722	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492724	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638354	1.00[ASN][1000 genomes]
rs72638356	1.00[ASN][1000 genomes]
rs7318105	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320230	1.00[ASN][1000 genomes]
rs7322453	0.80[CEU][hapmap]
rs7329965	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329985	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73546690	1.00[ASN][1000 genomes]
rs7981150	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984105	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7989918	1.00[ASN][1000 genomes]
rs7998457	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516431	1.00[ASN][1000 genomes]
rs9516436	0.80[CEU][hapmap]
rs9516439	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524564	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524575	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9524577	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9584241	1.00[ASN][1000 genomes]
rs9584242	1.00[ASN][1000 genomes]
rs9584243	1.00[ASN][1000 genomes]
rs9590039	0.80[CEU][hapmap]
rs9590043	0.81[CEU][hapmap]
rs9590045	1.00[ASN][1000 genomes]
rs9590046	1.00[ASN][1000 genomes]
rs9590048	1.00[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	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4417425	GPR180	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
2	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
5	chr13:95255800-95284000	Weak transcription	K562	blood
6	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:95264000-95284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
10	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
11	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
12	chr13:95264800-95284600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr13:95265400-95286800	Weak transcription	A549	lung
14	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr13:95268800-95283800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:95270000-95283400	Strong transcription	Dnd41	blood
17	chr13:95270400-95283400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:95270800-95283200	Strong transcription	Osteobl	bone
19	chr13:95271000-95283000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr13:95271000-95283600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:95272400-95282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:95272600-95283400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr13:95274000-95284400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr13:95275200-95282600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:95275200-95284000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr13:95275400-95283000	Strong transcription	NH-A	brain
27	chr13:95275400-95283200	Strong transcription	Fetal Thymus	thymus
28	chr13:95275400-95283400	Strong transcription	Adipose Nuclei	Adipose
29	chr13:95275800-95288800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr13:95276600-95292800	Weak transcription	Colon Smooth Muscle	Colon
31	chr13:95276600-95293600	Weak transcription	HSMMtube	muscle
32	chr13:95276800-95284400	Weak transcription	Fetal Lung	lung
33	chr13:95276800-95284800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr13:95276800-95285000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:95276800-95286000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:95276800-95286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:95276800-95287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr13:95276800-95287400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr13:95276800-95288600	Weak transcription	Primary T cells from cord blood	blood
40	chr13:95276800-95288800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr13:95276800-95289000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr13:95276800-95292400	Weak transcription	NHEK	skin
43	chr13:95276800-95292800	Weak transcription	NHLF	lung
44	chr13:95276800-95294000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr13:95277000-95286200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr13:95277000-95289200	Weak transcription	Brain Hippocampus Middle	brain
47	chr13:95277200-95283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:95277200-95283000	Weak transcription	Gastric	stomach
49	chr13:95277200-95283200	Weak transcription	Right Ventricle	heart
50	chr13:95277200-95285200	Weak transcription	Thymus	Thymus

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