Variant report

Variant	rs10055460
Chromosome Location	chr5:70910269-70910270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10044572	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10060578	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10064099	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10071645	0.81[ASN][1000 genomes]
rs10073617	0.81[ASN][1000 genomes]
rs10077085	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10434642	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10474383	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10805884	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10942533	0.82[EUR][1000 genomes]
rs10942682	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942700	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10942702	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10942705	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11746722	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12152748	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12516456	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12652715	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13157835	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2270920	0.81[ASN][1000 genomes]
rs4062889	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4505929	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62361818	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6452722	0.80[EUR][1000 genomes]
rs6452900	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6453014	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6453018	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6453035	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6453043	0.84[AMR][1000 genomes]
rs6871148	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6872235	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6872671	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6877289	0.80[EUR][1000 genomes]
rs6877773	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6886336	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6898471	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715747	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7378662	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7380115	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7380280	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7444322	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7448422	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7449316	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7714527	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7721179	0.84[EUR][1000 genomes]
rs9968768	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10055460	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
3	chr5:70893400-70916600	Weak transcription	Gastric	stomach
4	chr5:70893600-70930200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:70894000-70916400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:70895800-70910800	Weak transcription	Spleen	Spleen
7	chr5:70895800-70911600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:70895800-70937800	Weak transcription	Colonic Mucosa	Colon
9	chr5:70897000-70925800	Weak transcription	Right Ventricle	heart
10	chr5:70897200-70910800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:70897200-70911800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:70897200-70911800	Weak transcription	Fetal Brain Female	brain
13	chr5:70897200-70916600	Weak transcription	Esophagus	oesophagus
14	chr5:70897200-70930000	Weak transcription	Psoas Muscle	Psoas
15	chr5:70897400-70911800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:70897400-70921000	Weak transcription	Fetal Heart	heart
17	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:70897600-70910800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:70897600-70911400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:70897600-70911800	Weak transcription	Pancreas	Pancrea
21	chr5:70897800-70911400	Weak transcription	HSMMtube	muscle
22	chr5:70897800-70916400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
24	chr5:70898200-70944200	Weak transcription	Osteobl	bone
25	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
26	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:70898600-70915800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:70898600-70922400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
30	chr5:70899600-70911800	Weak transcription	Lung	lung
31	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:70900200-70911000	Weak transcription	HepG2	liver
33	chr5:70900200-70912000	Weak transcription	A549	lung
34	chr5:70900200-70912200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:70900200-70912400	Weak transcription	HSMM	muscle
36	chr5:70900200-70916600	Weak transcription	Hela-S3	cervix
37	chr5:70900200-70925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:70900200-70928200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:70900200-70930800	Weak transcription	HMEC	breast
40	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:70900400-70910800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:70900400-70910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:70900400-70910800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:70900400-70911200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:70900400-70911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr5:70900400-70911600	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:70900400-70911800	Weak transcription	Brain Anterior Caudate	brain
48	chr5:70900400-70912000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr5:70900400-70912600	Weak transcription	NHEK	skin
50	chr5:70900400-70916400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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