Variant report

Variant	rs10168293
Chromosome Location	chr2:54200930-54200931
allele	A/G
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:3)
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	chr2:54200823-54201033	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:54198564..54201435-chr2:54359737..54361960,2	K562	blood:
2	chr2:54074773..54076424-chr2:54200661..54203380,2	MCF-7	breast:
3	chr2:54196644..54199025-chr2:54199864..54201525,2	MCF-7	breast:
4	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
5	chr2:54200308..54201995-chr2:54341624..54344504,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-1	chr2:54200850-54200947	ENSG00000239235.3
2	lnc-ACYP2-1	chr2:54200850-54200947	ENSG00000239235.3
3	lnc-ACYP2-1	chr2:54200671-54200947	NONHSAT070714

No data

Variant related genes	Relation type
PSME4	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000265452	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10084374	0.82[EUR][1000 genomes]
rs10167891	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10181999	0.84[EUR][1000 genomes]
rs10183655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10186566	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11674724	0.85[ASN][1000 genomes]
rs11683741	0.94[ASN][1000 genomes]
rs11689025	0.94[ASN][1000 genomes]
rs11694711	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11893270	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13394278	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1477258	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045452	0.94[ASN][1000 genomes]
rs2112122	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28653587	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28851028	0.82[ASN][1000 genomes]
rs2909459	0.97[ASN][1000 genomes]
rs2949815	0.96[ASN][1000 genomes]
rs3731967	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671742	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671746	0.85[ASN][1000 genomes]
rs4671747	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55692047	0.87[ASN][1000 genomes]
rs56302494	0.86[ASN][1000 genomes]
rs62139336	0.94[ASN][1000 genomes]
rs6545377	0.87[ASN][1000 genomes]
rs6545380	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66773232	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6711105	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6711217	0.81[EUR][1000 genomes]
rs6715488	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6742042	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6743455	0.84[EUR][1000 genomes]
rs6746965	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6748976	0.87[ASN][1000 genomes]
rs6748997	0.85[ASN][1000 genomes]
rs72799298	0.87[ASN][1000 genomes]
rs72904908	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7559947	0.94[ASN][1000 genomes]
rs7564912	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7591431	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs805310	0.97[ASN][1000 genomes]
rs805344	0.97[ASN][1000 genomes]
rs805416	0.85[AMR][1000 genomes]
rs9631059	0.88[EUR][1000 genomes];0.87[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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10168293	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54209000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
3	chr2:54198800-54202600	Weak transcription	Lung	lung
4	chr2:54198800-54204200	Weak transcription	Esophagus	oesophagus
5	chr2:54198800-54205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54199000-54201000	Weak transcription	Placenta	Placenta
7	chr2:54199000-54201200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:54199000-54203200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:54199000-54203400	Weak transcription	Left Ventricle	heart
10	chr2:54199000-54203400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:54199000-54204200	Weak transcription	Thymus	Thymus
12	chr2:54199000-54207200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:54199000-54208600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
15	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
19	chr2:54199200-54201000	Weak transcription	NHEK	skin
20	chr2:54199200-54201200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:54199200-54201200	Weak transcription	Ovary	ovary
22	chr2:54199200-54201400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:54199200-54201400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:54199200-54201400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54199200-54201400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:54199200-54201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:54199200-54201400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:54199200-54201400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:54199200-54201400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:54199200-54201400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:54199200-54201400	Weak transcription	Adipose Nuclei	Adipose
32	chr2:54199200-54201400	Weak transcription	Liver	Liver
33	chr2:54199200-54201400	Weak transcription	Brain Angular Gyrus	brain
34	chr2:54199200-54201400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:54199200-54201400	Weak transcription	Fetal Lung	lung
36	chr2:54199200-54201400	Weak transcription	Fetal Thymus	thymus
37	chr2:54199200-54201400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:54199200-54201400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:54199200-54201400	Weak transcription	Osteobl	bone
40	chr2:54199200-54201600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr2:54199200-54201800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:54199200-54201800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:54199200-54202000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:54199200-54202000	Weak transcription	NHLF	lung
45	chr2:54199200-54202200	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:54199200-54202200	Weak transcription	Fetal Intestine Small	intestine
47	chr2:54199200-54202800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:54199200-54204200	Weak transcription	Pancreas	Pancrea
49	chr2:54199200-54204400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:54199200-54204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links