Variant report

Variant	rs6542060
Chromosome Location	chr2:113253252-113253253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113252098..113253969-chr2:113305095..113307068,2	MCF-7	breast:
2	chr2:113238650..113242491-chr2:113249319..113253275,7	MCF-7	breast:
3	chr2:113249787..113252552-chr2:113252556..113255186,2	K562	blood:

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10153801	0.82[EUR][1000 genomes]
rs11123137	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1127264	0.92[ASN][1000 genomes]
rs11644	0.92[ASN][1000 genomes]
rs11899598	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465241	0.92[ASN][1000 genomes]
rs12465446	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13030618	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043158	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17043167	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28542310	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34082454	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35419160	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849314	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3910512	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56010201	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62157527	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542059	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542061	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6718241	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6718489	0.92[ASN][1000 genomes]
rs6760014	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7569407	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580213	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6542060	RGPD8	cis	Artery Tibial	GTEx
rs6542060	RGPD8	cis	Nerve Tibial	GTEx
rs6542060	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6542060	TTL	cis	Skin Sun Exposed Lower leg	GTEx
rs6542060	RGPD8	cis	lung	GTEx
rs6542060	RGPD8	cis	Muscle Skeletal	GTEx
rs6542060	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6542060	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241000-113277200	Weak transcription	Gastric	stomach
2	chr2:113241000-113277800	Weak transcription	Colonic Mucosa	Colon
3	chr2:113241200-113259600	Weak transcription	Esophagus	oesophagus
4	chr2:113241200-113271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
6	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:113241400-113254000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:113241600-113260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
13	chr2:113241800-113257800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:113241800-113286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:113242000-113259600	Weak transcription	Fetal Heart	heart
17	chr2:113242400-113255600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:113244200-113254200	Strong transcription	Dnd41	blood
19	chr2:113244800-113259600	Weak transcription	GM12878-XiMat	blood
20	chr2:113245800-113277200	Weak transcription	Right Ventricle	heart
21	chr2:113245800-113277200	Weak transcription	Spleen	Spleen
22	chr2:113246200-113271600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:113250400-113253800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:113250600-113256200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:113250800-113253800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:113250800-113254600	Strong transcription	Fetal Thymus	thymus
27	chr2:113251000-113254200	Strong transcription	Fetal Brain Female	brain
28	chr2:113251400-113253400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:113251400-113253600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:113251400-113253800	Strong transcription	Fetal Stomach	stomach
31	chr2:113251400-113254200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:113251600-113253400	Strong transcription	Thymus	Thymus
33	chr2:113251600-113253600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:113251600-113253600	Strong transcription	Primary B cells from cord blood	blood
35	chr2:113251600-113253600	Strong transcription	Primary T cells from cord blood	blood
36	chr2:113251600-113253600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:113251600-113253800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:113251600-113253800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:113251600-113254000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:113251600-113259600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:113251800-113253400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:113251800-113253400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:113251800-113253800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:113251800-113253800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:113251800-113253800	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:113252000-113253600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:113252000-113253600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:113252000-113253600	Strong transcription	Liver	Liver
49	chr2:113252000-113253600	Strong transcription	NH-A	brain
50	chr2:113252000-113253800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links