Variant report

Variant	rs33551
Chromosome Location	chr5:112318928-112318929
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	POLR2A	chr5:112317933-112318957	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112238408..112240377-chr5:112318483..112320645,2	K562	blood:
2	chr5:112312385..112315007-chr5:112318753..112321264,2	MCF-7	breast:
3	chr5:112312383..112314551-chr5:112314826..112319334,4	MCF-7	breast:
4	chr5:112317791..112320092-chr5:112860829..112862554,2	K562	blood:

Variant related genes	Relation type
DCP2	TF binding region
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10058407	0.82[CHB][hapmap]
rs1057474	0.86[JPT][hapmap]
rs13156493	0.88[JPT][hapmap]
rs13177101	0.89[GIH][hapmap];0.82[JPT][hapmap]
rs13186334	0.91[GIH][hapmap];0.82[JPT][hapmap]
rs13445	0.86[GIH][hapmap]
rs1363333	0.86[JPT][hapmap];0.84[TSI][hapmap]
rs1549181	0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs17372511	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2112454	0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs2416300	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3185733	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs33543	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs33544	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33545	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33548	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33549	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33552	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33554	0.96[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33556	0.89[CHB][hapmap]
rs33557	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33558	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33559	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33560	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs33561	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33566	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33567	0.84[CHB][hapmap]
rs33568	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33569	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs3857434	0.86[JPT][hapmap]
rs4075350	0.86[JPT][hapmap]
rs4705749	0.87[GIH][hapmap];0.81[TSI][hapmap]
rs4705750	0.86[JPT][hapmap]
rs4705752	0.86[JPT][hapmap]
rs4778	0.82[JPT][hapmap]
rs7670	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs7701781	0.89[GIH][hapmap];0.86[JPT][hapmap]
rs9122	0.89[GIH][hapmap];0.86[JPT][hapmap]
rs9784647	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	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
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs33551	DCP2	Cis_1M	lymphoblastoid	RTeQTL
rs33551	MCC	cis	Whole Blood	GTEx
rs33551	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs33551	TSLP	cis	parietal	SCAN
rs33551	MCC	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
2	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:112314000-112320000	Weak transcription	Pancreas	Pancrea
4	chr5:112314000-112329000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:112314000-112335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:112314000-112337200	Weak transcription	Lung	lung
7	chr5:112314000-112338200	Weak transcription	Gastric	stomach
8	chr5:112314200-112319800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:112314200-112326800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:112314200-112328800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:112314200-112328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:112314200-112332000	Weak transcription	Fetal Kidney	kidney
13	chr5:112314200-112332000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
15	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
16	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
17	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
19	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
20	chr5:112314400-112322400	Weak transcription	Thymus	Thymus
21	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:112314800-112320000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:112314800-112322400	Weak transcription	Liver	Liver
24	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:112314800-112325800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:112314800-112332000	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:112314800-112332000	Weak transcription	NHLF	lung
29	chr5:112314800-112332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
32	chr5:112315400-112330800	Weak transcription	Brain Anterior Caudate	brain
33	chr5:112315600-112328600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:112315600-112332000	Weak transcription	NHDF-Ad	bronchial
35	chr5:112315600-112332200	Weak transcription	Ovary	ovary
36	chr5:112315600-112339400	Weak transcription	Hela-S3	cervix
37	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
38	chr5:112315800-112319200	Weak transcription	HUVEC	blood vessel
39	chr5:112315800-112319600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:112315800-112329200	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:112315800-112334600	Weak transcription	Brain Germinal Matrix	brain
42	chr5:112316000-112319000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr5:112316000-112332200	Weak transcription	Fetal Brain Female	brain
44	chr5:112316000-112337000	Weak transcription	A549	lung
45	chr5:112316200-112319800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:112316200-112324600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:112316400-112319400	Genic enhancers	Dnd41	blood
48	chr5:112316400-112324200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:112316400-112330000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:112316600-112320000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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