Variant report

Variant	rs10940218
Chromosome Location	chr5:68625460-68625461
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68623977..68626079-chr5:68626593..68628678,2	K562	blood:
2	chr5:68591369..68594137-chr5:68623717..68625664,2	MCF-7	breast:
3	chr5:68514182..68515689-chr5:68624413..68626099,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183323	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10044508	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10045361	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10471350	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471774	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10471775	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10471776	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10940212	0.82[EUR][1000 genomes]
rs10940216	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11748974	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12187268	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188076	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517724	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178839	0.80[EUR][1000 genomes]
rs13361598	0.81[EUR][1000 genomes]
rs1530290	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010352	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28580747	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34935424	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4252228	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4473723	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976160	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4976189	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4976190	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4976194	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58772585	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62373187	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6450029	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6450032	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873869	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6875069	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6879078	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7708429	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712318	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9291947	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291948	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791036	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10940218	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs10940218	CCDC125	cis	lung	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
3	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
5	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
6	chr5:68577600-68627400	Weak transcription	NHEK	skin
7	chr5:68577800-68626600	Weak transcription	A549	lung
8	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
10	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
11	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:68599600-68627800	Weak transcription	NH-A	brain
14	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:68605600-68627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:68606200-68625600	Weak transcription	Hela-S3	cervix
17	chr5:68609600-68627400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:68609600-68627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:68609800-68627200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:68609800-68627400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:68609800-68627400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:68609800-68627400	Weak transcription	Esophagus	oesophagus
23	chr5:68609800-68627400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:68609800-68627400	Weak transcription	GM12878-XiMat	blood
25	chr5:68609800-68627600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:68609800-68627600	Weak transcription	Fetal Thymus	thymus
27	chr5:68609800-68628200	Weak transcription	Right Ventricle	heart
28	chr5:68609800-68628400	Weak transcription	Lung	lung
29	chr5:68610000-68627400	Weak transcription	Dnd41	blood
30	chr5:68610400-68627600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr5:68610600-68627800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:68611000-68628200	Weak transcription	Aorta	Aorta
33	chr5:68612400-68627400	Weak transcription	Adipose Nuclei	Adipose
34	chr5:68612800-68626600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:68613800-68627200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:68613800-68627400	Weak transcription	Primary B cells from cord blood	blood
37	chr5:68614200-68627400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:68616200-68626600	Weak transcription	Colonic Mucosa	Colon
39	chr5:68616400-68627400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:68616600-68628200	Weak transcription	Left Ventricle	heart
41	chr5:68616800-68627200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr5:68617000-68627400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:68617000-68627600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:68617400-68627400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:68617600-68626400	Weak transcription	Liver	Liver
46	chr5:68618000-68627400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:68620800-68626400	Weak transcription	Stomach Mucosa	stomach
48	chr5:68621000-68628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:68621400-68627600	Weak transcription	Primary T cells from cord blood	blood
50	chr5:68622000-68627400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links