Variant report

Variant	rs2972388
Chromosome Location	chr5:68531253-68531254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68483901..68487830-chr5:68528757..68532922,9	K562	blood:
2	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:
3	chr5:68529171..68532388-chr5:68663415..68666737,3	K562	blood:
4	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
5	chr5:68530945..68532461-chr5:68661059..68663307,2	K562	blood:
6	chr5:68512209..68515422-chr5:68529314..68532677,7	MCF-7	breast:
7	chr5:68530475..68532147-chr5:89705204..89707833,2	MCF-7	breast:
8	chr5:68529975..68532202-chr5:68627120..68629377,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS36-2	chr5:68531221-68531280	NONHSAT101904
2	lnc-MRPS36-2	chr5:68531221-68531322	NONHSAT101905

No data

Variant related genes	Relation type
ENSG00000152942	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10063757	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10940209	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940210	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10940212	0.81[ASN][1000 genomes]
rs10940216	0.81[ASN][1000 genomes]
rs11744596	0.80[ASN][1000 genomes]
rs11748974	0.89[ASN][1000 genomes]
rs12659146	0.80[ASN][1000 genomes]
rs13175606	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151589	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs163444	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164709	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs164715	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164789	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1650779	0.87[ASN][1000 genomes]
rs171212	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184747	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976103	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2002825	0.80[ASN][1000 genomes]
rs2130757	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2171148	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172056	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242350	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2242351	0.80[ASN][1000 genomes]
rs2291519	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291520	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450230	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450246	0.85[ASN][1000 genomes]
rs28602964	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28768211	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2930944	0.80[ASN][1000 genomes]
rs2930945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930946	0.80[ASN][1000 genomes]
rs2930949	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930951	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932767	0.85[ASN][1000 genomes]
rs2932770	0.80[ASN][1000 genomes]
rs2932771	0.80[ASN][1000 genomes]
rs2932772	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932774	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2932775	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932776	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932777	0.80[ASN][1000 genomes]
rs2932778	0.81[ASN][1000 genomes]
rs2932780	0.84[ASN][1000 genomes]
rs2932782	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932783	0.84[ASN][1000 genomes]
rs2972358	0.80[ASN][1000 genomes]
rs2972361	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972366	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972373	0.80[ASN][1000 genomes]
rs2972374	0.80[ASN][1000 genomes]
rs2972377	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972378	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972381	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972386	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972387	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972390	0.80[ASN][1000 genomes]
rs34893396	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34935424	0.85[ASN][1000 genomes]
rs350104	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350106	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350107	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350109	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350115	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350116	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350122	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350124	0.80[ASN][1000 genomes]
rs351424	0.88[ASN][1000 genomes]
rs35308484	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs353656	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs379106	0.88[ASN][1000 genomes]
rs386640	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934528	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077460	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs419902	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs426392	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4266362	0.90[ASN][1000 genomes]
rs4362903	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4421064	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4541612	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4629549	0.92[ASN][1000 genomes]
rs488498	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4976189	0.84[ASN][1000 genomes]
rs603029	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62373164	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6450026	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6450027	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6450029	0.85[ASN][1000 genomes]
rs651076	0.86[ASN][1000 genomes]
rs676012	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs676879	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6862253	0.83[ASN][1000 genomes]
rs6866993	0.92[ASN][1000 genomes]
rs6873869	0.85[ASN][1000 genomes]
rs6876783	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs693725	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7733556	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2972388	CCDC125	cis	lung	GTEx
rs2972388	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2972388	CCDC125	cis	Muscle Skeletal	GTEx
rs2972388	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2972388	GUSBP3	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68529800-68532000	Active TSS	A549	lung
2	chr5:68529800-68533000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:68530000-68531400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:68530000-68531400	Active TSS	Fetal Brain Male	brain
5	chr5:68530000-68531400	Active TSS	Fetal Stomach	stomach
6	chr5:68530000-68531400	Active TSS	Right Ventricle	heart
7	chr5:68530000-68531400	Active TSS	Thymus	Thymus
8	chr5:68530000-68531600	Active TSS	Fetal Muscle Leg	muscle
9	chr5:68530000-68531600	Active TSS	Fetal Thymus	thymus
10	chr5:68530000-68531600	Active TSS	Rectal Smooth Muscle	rectum
11	chr5:68530000-68531800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:68530000-68531800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr5:68530000-68531800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:68530000-68531800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:68530000-68532200	Active TSS	Psoas Muscle	Psoas
16	chr5:68530000-68532400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr5:68530000-68532600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:68530200-68531400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr5:68530200-68531400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:68530200-68531400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:68530200-68531400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr5:68530200-68531400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:68530200-68531400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:68530200-68531400	Active TSS	Muscle Satellite Cultured Cells	--
25	chr5:68530200-68531400	Active TSS	Aorta	Aorta
26	chr5:68530200-68531400	Active TSS	Brain Angular Gyrus	brain
27	chr5:68530200-68531400	Active TSS	Brain Anterior Caudate	brain
28	chr5:68530200-68531400	Active TSS	Brain Cingulate Gyrus	brain
29	chr5:68530200-68531400	Active TSS	Brain Hippocampus Middle	brain
30	chr5:68530200-68531400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr5:68530200-68531400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr5:68530200-68531400	Active TSS	Fetal Brain Female	brain
33	chr5:68530200-68531400	Active TSS	Fetal Lung	lung
34	chr5:68530200-68531400	Active TSS	HUVEC	blood vessel
35	chr5:68530200-68531600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:68530200-68531600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr5:68530200-68531600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:68530200-68531600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:68530200-68531600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:68530200-68531600	Active TSS	Brain Substantia Nigra	brain
41	chr5:68530200-68531600	Active TSS	Colonic Mucosa	Colon
42	chr5:68530200-68531600	Active TSS	Fetal Muscle Trunk	muscle
43	chr5:68530200-68531600	Active TSS	Ovary	ovary
44	chr5:68530200-68531800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:68530200-68531800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:68530200-68531800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr5:68530200-68531800	Active TSS	Fetal Intestine Small	intestine
48	chr5:68530200-68531800	Active TSS	Right Atrium	heart
49	chr5:68530200-68531800	Active TSS	Stomach Mucosa	stomach
50	chr5:68530200-68531800	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links