Variant report

Variant	rs892118
Chromosome Location	chr19:40774253-40774254
allele	C/T
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:0)
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	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:40770481..40772610-chr19:40774016..40777021,3	K562	blood:
2	chr19:40774152..40777118-chr19:40779107..40782198,3	MCF-7	breast:
3	chr19:40772625..40774748-chr19:40789587..40791342,2	MCF-7	breast:
4	chr19:40766133..40769095-chr19:40773189..40775084,2	K562	blood:
5	chr19:40772355..40774714-chr19:40778588..40781448,2	MCF-7	breast:

No data

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105221	Chromatin interaction
ENSG00000205041	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10408356	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10415181	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10416620	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10418932	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10419465	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420842	0.91[EUR][1000 genomes]
rs10422343	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs10423896	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12151243	0.95[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs16974157	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163840	0.92[ASN][1000 genomes]
rs2304188	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28362958	0.86[ASN][1000 genomes]
rs28667591	0.93[EUR][1000 genomes]
rs34716810	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55862427	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57885763	0.92[EUR][1000 genomes]
rs58336440	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58613082	0.92[EUR][1000 genomes]
rs59010363	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59343080	0.89[ASN][1000 genomes]
rs60869669	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61685259	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62107590	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107593	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62107594	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62107630	0.93[EUR][1000 genomes]
rs62107631	0.93[EUR][1000 genomes]
rs7247916	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7248861	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7254617	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8100207	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8111619	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8112998	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs892119	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs892120	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9304588	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9304589	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs934426	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1064502	chr19:40758049-40781360	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1063993	chr19:40763787-40781360	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059884	chr19:40763839-40781360	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs892118	EML2	cis	cerebellum	SCAN
rs892118	DEDD2	cis	cerebellum	SCAN
rs892118	APOC4	cis	cerebellum	SCAN
rs892118	RPL18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40759800-40775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:40759800-40780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:40762000-40779800	Weak transcription	Stomach Mucosa	stomach
4	chr19:40762800-40777600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:40762800-40780800	Weak transcription	Small Intestine	intestine
6	chr19:40763600-40777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:40763800-40777600	Weak transcription	Hela-S3	cervix
8	chr19:40763800-40777600	Weak transcription	HMEC	breast
9	chr19:40765400-40777800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
11	chr19:40766800-40776600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:40767000-40776200	Strong transcription	Primary T cells from cord blood	blood
13	chr19:40767400-40774800	Strong transcription	Thymus	Thymus
14	chr19:40767600-40774800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:40767600-40779600	Strong transcription	Fetal Stomach	stomach
16	chr19:40767800-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:40768000-40774400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:40768200-40774600	Strong transcription	Fetal Intestine Large	intestine
19	chr19:40768200-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:40769000-40776600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr19:40769000-40778200	Weak transcription	HSMM	muscle
22	chr19:40769000-40779600	Strong transcription	Fetal Intestine Small	intestine
23	chr19:40769400-40777400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:40769600-40776200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:40769600-40783600	Weak transcription	Fetal Kidney	kidney
26	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:40770200-40775000	Enhancers	Brain Angular Gyrus	brain
29	chr19:40770200-40776200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
32	chr19:40770400-40784000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:40770600-40774800	Enhancers	Brain Substantia Nigra	brain
34	chr19:40770600-40775000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr19:40771000-40777600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:40771000-40780400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:40771000-40780800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr19:40771000-40783600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:40771200-40774600	Enhancers	Psoas Muscle	Psoas
40	chr19:40771200-40774800	Enhancers	Right Atrium	heart
41	chr19:40771200-40775000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr19:40771200-40775600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:40771200-40776000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:40771200-40776000	Weak transcription	Fetal Lung	lung
45	chr19:40771200-40776200	Enhancers	Brain Anterior Caudate	brain
46	chr19:40771200-40776200	Weak transcription	Fetal Thymus	thymus
47	chr19:40771200-40776200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:40771200-40776400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:40771200-40777600	Weak transcription	Osteobl	bone
50	chr19:40771200-40778000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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