Variant report

Variant	rs4252228
Chromosome Location	chr5:68662136-68662137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68659738-68662513	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68637589..68639798-chr5:68660289..68662388,2	MCF-7	breast:
2	chr5:68626792..68633026-chr5:68660168..68667090,13	MCF-7	breast:
3	chr5:68644789..68648896-chr5:68660361..68665573,5	K562	blood:
4	chr5:68626462..68633259-chr5:68656360..68665608,14	MCF-7	breast:
5	chr5:68530945..68532461-chr5:68661059..68663307,2	K562	blood:

No data

Variant related genes	Relation type
RAD17	TF binding region
ENSG00000134058	Chromatin interaction
ENSG00000215006	Chromatin interaction
ENSG00000271045	Chromatin interaction
ENSG00000183323	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10035835	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10038816	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10044508	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10045361	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10055160	0.86[EUR][1000 genomes]
rs10064264	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10068576	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077458	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10078100	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10471350	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10471774	0.90[AFR][1000 genomes]
rs10471775	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10471776	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10940218	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1168404	0.88[ASN][1000 genomes]
rs1168409	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1177556	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1183278	0.89[ASN][1000 genomes]
rs12187268	0.80[EUR][1000 genomes]
rs12188076	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12517724	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1530290	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2010352	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2561172	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2561186	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28580747	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28703034	0.81[ASN][1000 genomes]
rs299075	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299077	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299088	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299091	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299094	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299098	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs299099	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299102	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4473723	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4976160	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4976194	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58772585	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62373187	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6450032	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6875069	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6879078	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7708429	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7712318	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9291947	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9291948	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9791036	0.82[AMR][1000 genomes];0.82[EUR][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	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4252228	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs4252228	MRPS36	cis	lymphoblastoid	seeQTL
rs4252228	CCDC125	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68639200-68663400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:68643000-68664400	Weak transcription	Colonic Mucosa	Colon
3	chr5:68643200-68663200	Weak transcription	Small Intestine	intestine
4	chr5:68643800-68663600	Weak transcription	Brain Angular Gyrus	brain
5	chr5:68645800-68663400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:68647400-68663400	Weak transcription	Fetal Brain Male	brain
7	chr5:68647400-68663800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:68648400-68663400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:68649200-68663600	Weak transcription	Brain Substantia Nigra	brain
10	chr5:68649400-68663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:68651400-68663600	Weak transcription	Right Ventricle	heart
12	chr5:68651400-68664400	Weak transcription	Aorta	Aorta
13	chr5:68653200-68664600	Weak transcription	Esophagus	oesophagus
14	chr5:68654400-68663200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr5:68654800-68663400	Strong transcription	Fetal Muscle Leg	muscle
16	chr5:68655600-68662400	Strong transcription	Primary T cells from cord blood	blood
17	chr5:68656000-68663400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:68656000-68663400	Strong transcription	Fetal Thymus	thymus
19	chr5:68657000-68663200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:68657800-68663200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:68657800-68663200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:68657800-68663400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:68657800-68663400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr5:68658000-68662200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:68658000-68662400	Strong transcription	HUVEC	blood vessel
26	chr5:68658000-68662400	Strong transcription	K562	blood
27	chr5:68658000-68662600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:68658000-68663000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:68658000-68663000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:68658000-68663000	Strong transcription	Liver	Liver
31	chr5:68658000-68663200	Strong transcription	Primary B cells from cord blood	blood
32	chr5:68658000-68663200	Strong transcription	Placenta	Placenta
33	chr5:68658000-68663400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:68658000-68663400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:68658000-68663400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:68658200-68662600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr5:68658200-68662600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:68658200-68662600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:68658200-68663000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:68658200-68663000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:68658200-68663200	Strong transcription	Adipose Nuclei	Adipose
42	chr5:68658200-68663200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:68658200-68663400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:68658200-68663400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:68658200-68663400	Strong transcription	Fetal Intestine Large	intestine
46	chr5:68658400-68663000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:68658400-68663000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:68658400-68663000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:68658400-68663200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:68658600-68662200	Strong transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links