Variant report

Variant	rs11083642
Chromosome Location	chr19:42461454-42461455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42430426..42435985-chr19:42461209..42463660,4	K562	blood:
2	chr19:42459797..42462161-chr19:42571627..42574453,2	MCF-7	breast:
3	chr19:42381223..42383832-chr19:42460147..42462553,2	MCF-7	breast:
4	chr19:42361051..42365836-chr19:42460461..42465209,10	K562	blood:
5	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:
6	chr19:42461278..42463492-chr20:55838965..55841655,2	MCF-7	breast:
7	chr19:42361938..42366462-chr19:42459916..42465209,13	K562	blood:
8	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
9	chr19:42460531..42463518-chr19:42578179..42580939,2	K562	blood:
10	chr19:42460466..42464604-chr19:42577075..42581382,5	MCF-7	breast:
11	chr19:42385735..42391033-chr19:42460351..42463651,6	K562	blood:
12	chr19:42385036..42390018-chr19:42460408..42463391,5	K562	blood:
13	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RABAC1-1	chr19:42461170-42461651	NONHSAT066507

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000105737	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105372	Chromatin interaction
ENSG00000105369	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10409822	0.88[ASN][1000 genomes]
rs10411814	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10416501	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10419731	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10420264	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10424013	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11665965	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11667048	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668332	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11669448	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11878287	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12971376	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972751	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12975677	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864207	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1965727	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2081999	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745223	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826707	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61007366	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246830	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247727	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253563	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs735571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109192	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919390	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9304600	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9676662	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9749440	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11083642	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs11083642	RABAC1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42445600-42462400	Weak transcription	Right Atrium	heart
2	chr19:42451200-42461600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:42451200-42462000	Weak transcription	Primary T cells from cord blood	blood
4	chr19:42455800-42462400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:42456000-42462000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:42456200-42461600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:42456200-42461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:42456200-42461600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:42456200-42461600	Weak transcription	Brain Angular Gyrus	brain
10	chr19:42456200-42461600	Weak transcription	GM12878-XiMat	blood
11	chr19:42456200-42461600	Weak transcription	HSMM	muscle
12	chr19:42456200-42461800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:42456200-42461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:42456200-42461800	Weak transcription	Primary B cells from cord blood	blood
15	chr19:42456200-42461800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:42456200-42461800	Weak transcription	Fetal Lung	lung
17	chr19:42456200-42462000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:42456200-42462000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr19:42456200-42462000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:42456200-42462200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:42456200-42462200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:42456200-42462400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:42458400-42461800	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:42458400-42462200	Weak transcription	HSMMtube	muscle
25	chr19:42458800-42462200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr19:42459200-42461600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:42459200-42461600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:42459200-42461600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:42459200-42461800	Strong transcription	Thymus	Thymus
30	chr19:42459400-42461600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:42459600-42461600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:42459600-42461600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr19:42459600-42461600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:42459600-42461600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr19:42459800-42461600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:42459800-42461600	Strong transcription	NHLF	lung
37	chr19:42459800-42461800	Strong transcription	Brain Cingulate Gyrus	brain
38	chr19:42459800-42461800	Enhancers	Stomach Mucosa	stomach
39	chr19:42460000-42461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:42460000-42461600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:42460000-42461600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:42460000-42461600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:42460000-42461600	Strong transcription	Fetal Brain Female	brain
44	chr19:42460000-42461600	Weak transcription	Fetal Heart	heart
45	chr19:42460000-42462400	Weak transcription	Psoas Muscle	Psoas
46	chr19:42460200-42461600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:42460200-42461600	Strong transcription	Pancreas	Pancrea
48	chr19:42460200-42461600	Strong transcription	Dnd41	blood
49	chr19:42460400-42461600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:42460400-42461800	Strong transcription	Fetal Thymus	thymus

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