Variant report

Variant	rs818425
Chromosome Location	chr5:112226655-112226656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112225010..112227732-chr5:112311163..112313003,2	K562	blood:
2	chr5:112223765..112227904-chr5:112256681..112259724,3	K562	blood:

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1069061	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1093611	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1093677	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1441375	0.81[CEU][hapmap]
rs151976	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151977	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151978	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153545	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153546	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs153548	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs153550	0.86[EUR][1000 genomes]
rs1661035	0.84[CEU][hapmap]
rs193527	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545162	0.84[CEU][hapmap]
rs2545163	0.84[CEU][hapmap]
rs2545166	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545167	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545169	0.84[CEU][hapmap]
rs2909904	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs351767	0.92[EUR][1000 genomes]
rs351769	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351770	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs35726351	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs368575	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs372492	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs380144	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs382260	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs386830	0.87[ASN][1000 genomes]
rs392907	0.85[CEU][hapmap]
rs397768	0.84[ASN][1000 genomes]
rs411356	0.84[CEU][hapmap]
rs419632	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs429427	0.92[CEU][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs430665	0.88[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs431287	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs433429	0.87[ASN][1000 genomes]
rs434090	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs434157	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs438252	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs439456	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs442507	0.81[EUR][1000 genomes]
rs446567	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs448162	0.80[CEU][hapmap]
rs455412	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455469	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs456313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs458451	0.89[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459102	0.92[EUR][1000 genomes]
rs460301	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs460832	0.88[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461424	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461866	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs463229	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs464002	0.84[CEU][hapmap]
rs464708	0.84[CEU][hapmap]
rs465454	1.00[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs465899	0.83[ASN][1000 genomes]
rs466443	0.86[ASN][1000 genomes]
rs468101	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs468610	0.85[EUR][1000 genomes]
rs468783	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs468854	0.85[EUR][1000 genomes]
rs469663	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs469727	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs469760	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs469827	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs481789	0.85[ASN][1000 genomes]
rs495794	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs497844	0.80[CEU][hapmap];0.89[ASN][1000 genomes]
rs514763	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs519397	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs563556	0.81[CEU][hapmap]
rs565453	0.87[ASN][1000 genomes]
rs565603	0.89[ASN][1000 genomes]
rs580237	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs698405	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712662	0.88[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712663	0.88[EUR][1000 genomes]
rs712664	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs712665	0.88[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712666	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712668	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712671	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs818423	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs818424	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818426	0.95[ASN][1000 genomes]
rs818427	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs818429	0.92[EUR][1000 genomes]
rs864682	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9011	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	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
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv3470639	chr5:112222353-112227151	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	esv3470640	chr5:112224115-112226988	Weak transcription Enhancers Genic enhancers Strong transcription	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	esv3470638	chr5:112224168-112226958	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	esv3470642	chr5:112224236-112226890	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs818425	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
3	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
6	chr5:112211200-112240000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:112211800-112239200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:112212600-112251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:112213200-112229400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:112214200-112232200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:112214800-112234800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:112215200-112255800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:112215800-112240400	Strong transcription	Primary B cells from cord blood	blood
16	chr5:112215800-112247200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:112216400-112226800	Strong transcription	Dnd41	blood
18	chr5:112219800-112232200	Strong transcription	Fetal Intestine Small	intestine
19	chr5:112221400-112237800	Weak transcription	Small Intestine	intestine
20	chr5:112221800-112231400	Weak transcription	Psoas Muscle	Psoas
21	chr5:112221800-112231800	Weak transcription	Stomach Mucosa	stomach
22	chr5:112221800-112256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112222000-112231400	Weak transcription	Hela-S3	cervix
24	chr5:112222000-112233800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:112222000-112256400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:112222200-112229200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:112222200-112231200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:112222800-112229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:112222800-112229600	Weak transcription	Fetal Heart	heart
30	chr5:112222800-112231600	Weak transcription	Fetal Kidney	kidney
31	chr5:112222800-112239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:112223000-112227400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:112223000-112227400	Weak transcription	Gastric	stomach
34	chr5:112223000-112227400	Weak transcription	Spleen	Spleen
35	chr5:112223000-112227600	Weak transcription	Brain Hippocampus Middle	brain
36	chr5:112223000-112227800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:112223000-112227800	Weak transcription	Esophagus	oesophagus
38	chr5:112223000-112228000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:112223000-112228000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:112223000-112228000	Weak transcription	NHLF	lung
41	chr5:112223000-112228200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:112223000-112228200	Weak transcription	Lung	lung
43	chr5:112223000-112229200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:112223000-112229200	Weak transcription	Brain Angular Gyrus	brain
45	chr5:112223000-112229200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:112223000-112231000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:112223000-112231200	Weak transcription	Brain Substantia Nigra	brain
48	chr5:112223000-112231200	Weak transcription	HUVEC	blood vessel
49	chr5:112223000-112231400	Weak transcription	HSMMtube	muscle
50	chr5:112223000-112233600	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links