Variant report

Variant	rs7670
Chromosome Location	chr5:112356649-112356650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112356556..112358824-chr5:112361701..112363317,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10039618	0.80[JPT][hapmap]
rs1057474	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12517398	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12654474	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13156493	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13159449	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13171553	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13171773	0.82[EUR][1000 genomes]
rs13176362	0.80[EUR][1000 genomes]
rs13177101	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13183347	0.82[EUR][1000 genomes]
rs13186334	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13445	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1363333	0.87[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1549181	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17312754	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17372511	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2112454	0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs2416300	0.91[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap]
rs3185733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33544	0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs33551	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs33552	0.90[JPT][hapmap]
rs33554	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs33557	0.85[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap]
rs33568	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs33569	0.80[TSI][hapmap]
rs3857434	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4075350	0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4334876	0.85[EUR][1000 genomes]
rs4705529	0.80[EUR][1000 genomes]
rs4705744	0.81[EUR][1000 genomes]
rs4705745	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4705749	0.87[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705750	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4705752	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4778	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6869100	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6893389	0.81[JPT][hapmap]
rs7701781	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7732198	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs9122	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9784647	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv964924	chr5:112353388-112356719	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7670	DCP2	cis	Nerve Tibial	GTEx
rs7670	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs7670	TSLP	cis	parietal	SCAN
rs7670	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs7670	DCP2	cis	lymphoblastoid	seeQTL
rs7670	MCC	cis	Whole Blood	GTEx
rs7670	MCC	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
2	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
3	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
4	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
12	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
13	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:112329400-112356800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr5:112330200-112362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
18	chr5:112333000-112359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:112333200-112362400	Weak transcription	Right Ventricle	heart
20	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
21	chr5:112338600-112360800	Weak transcription	Aorta	Aorta
22	chr5:112339200-112362400	Weak transcription	Pancreas	Pancrea
23	chr5:112339400-112362000	Weak transcription	Gastric	stomach
24	chr5:112340400-112362400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:112340400-112362600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:112340400-112362600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:112341600-112357600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:112342200-112362600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr5:112343200-112357000	Strong transcription	Primary B cells from cord blood	blood
30	chr5:112343200-112357000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:112349800-112359600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:112349800-112362400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:112349800-112366600	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:112350000-112360600	Weak transcription	Fetal Intestine Small	intestine
35	chr5:112350200-112358000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:112350200-112361400	Weak transcription	Brain Substantia Nigra	brain
37	chr5:112350200-112361400	Weak transcription	Lung	lung
38	chr5:112350200-112361400	Weak transcription	Ovary	ovary
39	chr5:112350200-112362000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr5:112350200-112362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:112350200-112362600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:112350200-112362600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:112350200-112362600	Weak transcription	Brain Anterior Caudate	brain
44	chr5:112350200-112362800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:112350400-112358400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:112350400-112359800	Weak transcription	Left Ventricle	heart
47	chr5:112350400-112360800	Weak transcription	Fetal Intestine Large	intestine
48	chr5:112350400-112361000	Weak transcription	Fetal Stomach	stomach
49	chr5:112350400-112361400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:112350400-112361800	Weak transcription	Brain Hippocampus Middle	brain

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