Variant report

Variant	rs17312754
Chromosome Location	chr5:112336634-112336635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr5:112336125-112336677	SK-N-SH	brain:	n/a	chr5:112336380-112336387 chr5:112336382-112336390 chr5:112336355-112336364 chr5:112336380-112336392
2	TCF12	chr5:112336065-112336712	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:112336582-112336655	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:112335887-112336756	K562	blood:	n/a	n/a

Variant related genes	Relation type
DCP2	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12517398	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12654474	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156493	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13159449	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13171553	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13171773	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13176362	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13177101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183347	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13186334	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13445	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363333	0.84[AFR][1000 genomes]
rs1549182	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17372511	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2112454	0.87[ASN][1000 genomes]
rs3185733	0.87[EUR][1000 genomes]
rs33544	0.86[ASN][1000 genomes]
rs33545	0.86[ASN][1000 genomes]
rs33548	0.86[ASN][1000 genomes]
rs3857434	0.83[EUR][1000 genomes]
rs4075350	0.81[EUR][1000 genomes]
rs4334876	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4705529	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705531	0.83[AMR][1000 genomes]
rs4705744	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705745	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4705749	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705750	0.81[EUR][1000 genomes]
rs4705752	0.83[EUR][1000 genomes]
rs4778	0.91[EUR][1000 genomes]
rs6869100	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7670	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7701781	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9122	0.83[EUR][1000 genomes]
rs9784647	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17312754	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs17312754	MCC	cis	Whole Blood	GTEx
rs17312754	DCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112314000-112337200	Weak transcription	Lung	lung
3	chr5:112314000-112338200	Weak transcription	Gastric	stomach
4	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
5	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
6	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
7	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
9	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
10	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
13	chr5:112315600-112339400	Weak transcription	Hela-S3	cervix
14	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:112316000-112337000	Weak transcription	A549	lung
16	chr5:112317000-112338200	Weak transcription	Left Ventricle	heart
17	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:112319400-112336800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:112320200-112338200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:112320200-112338200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:112320600-112337200	Weak transcription	Pancreas	Pancrea
25	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:112321600-112353800	Weak transcription	Fetal Heart	heart
29	chr5:112322200-112341000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
31	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
32	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:112326000-112336800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:112326800-112337000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:112327400-112340600	Strong transcription	Primary B cells from cord blood	blood
36	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:112328800-112341800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:112330200-112337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:112330200-112338200	Weak transcription	Spleen	Spleen
41	chr5:112330200-112362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:112330400-112336800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:112330600-112337000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:112330800-112337200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:112331200-112337800	Weak transcription	Brain Anterior Caudate	brain
46	chr5:112331800-112337200	Weak transcription	Fetal Muscle Leg	muscle
47	chr5:112332200-112336800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr5:112332400-112336800	Weak transcription	HUVEC	blood vessel
49	chr5:112332400-112348600	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:112332400-112352400	Strong transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links