Variant report

Variant	rs1055583
Chromosome Location	chr10:50226334-50226335
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50225099..50226712-chr10:50226883..50229735,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1877804	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877805	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1913518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913519	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1913521	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996185	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2137920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2175918	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2243994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244575	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs2244967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245145	0.95[ASN][1000 genomes]
rs2245147	0.95[ASN][1000 genomes]
rs2245149	0.95[ASN][1000 genomes]
rs2245162	0.95[ASN][1000 genomes]
rs2245165	0.92[ASN][1000 genomes]
rs2253873	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254384	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2254393	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254409	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2254410	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254412	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254617	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254628	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254740	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2254754	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254863	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2255253	0.96[ASN][1000 genomes]
rs2255360	0.98[ASN][1000 genomes]
rs2255739	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255943	0.96[ASN][1000 genomes]
rs2264555	0.96[ASN][1000 genomes]
rs2264844	0.96[ASN][1000 genomes]
rs2264848	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2264849	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2458672	0.96[ASN][1000 genomes]
rs2466751	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2466752	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2466754	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2466755	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725199	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2955063	0.95[ASN][1000 genomes]
rs883017	0.98[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1055583	C10orf72	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50217200-50226600	Weak transcription	Aorta	Aorta
2	chr10:50217400-50231200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:50217600-50227000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:50218600-50238200	Weak transcription	Esophagus	oesophagus
5	chr10:50218800-50231400	Weak transcription	Adipose Nuclei	Adipose
6	chr10:50219200-50226600	Weak transcription	HSMMtube	muscle
7	chr10:50220400-50233600	Weak transcription	Gastric	stomach
8	chr10:50220800-50231200	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:50221000-50233400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:50221800-50226600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr10:50221800-50227400	Weak transcription	Fetal Intestine Small	intestine
12	chr10:50221800-50231400	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:50221800-50232400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:50222000-50231400	Weak transcription	Right Ventricle	heart
15	chr10:50222000-50233800	Weak transcription	Lung	lung
16	chr10:50222200-50226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:50222800-50279000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr10:50223000-50226600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:50223000-50226600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr10:50223000-50226800	Weak transcription	Ovary	ovary
21	chr10:50223000-50231600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:50223000-50231600	Weak transcription	Left Ventricle	heart
23	chr10:50223000-50254200	Weak transcription	NHDF-Ad	bronchial
24	chr10:50223200-50226800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:50223600-50226400	Strong transcription	Fetal Stomach	stomach
26	chr10:50223600-50227800	Strong transcription	Fetal Muscle Leg	muscle
27	chr10:50223600-50228000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr10:50223800-50227600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr10:50223800-50227800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr10:50224200-50228000	Strong transcription	Fetal Lung	lung
31	chr10:50224200-50231600	Weak transcription	Fetal Kidney	kidney
32	chr10:50224400-50258200	Weak transcription	Brain Anterior Caudate	brain
33	chr10:50224600-50244800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:50225200-50227400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:50225200-50227800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:50225800-50231200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links