Variant report

Variant	rs833829
Chromosome Location	chr12:49352319-49352320
allele	C/T
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:0)
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	chr12:49352012..49353906-chr12:49367184..49368972,2	MCF-7	breast:
2	chr12:49326822..49334011-chr12:49345841..49353556,12	MCF-7	breast:
3	chr12:49349007..49352698-chr12:49523718..49526243,3	K562	blood:
4	chr12:49350460..49352797-chr12:49389222..49392992,4	MCF-7	breast:
5	chr12:49317412..49320697-chr12:49349793..49352537,4	MCF-7	breast:
6	chr12:49244090..49248564-chr12:49349147..49352476,5	MCF-7	breast:
7	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
8	chr12:49244315..49247663-chr12:49350223..49353820,7	MCF-7	breast:
9	chr12:49349743..49353633-chr12:49353636..49360057,10	MCF-7	breast:
10	chr12:49348804..49352502-chr12:49411258..49414497,4	MCF-7	breast:
11	chr12:49351134..49353553-chr12:49353996..49358640,5	MCF-7	breast:
12	chr12:49349770..49352703-chr12:49396550..49398736,3	K562	blood:
13	chr12:49351084..49352752-chr12:49363357..49365742,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174243	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000238395	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000169884	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11168810	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12122	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12829682	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2694841	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41291977	0.86[EUR][1000 genomes]
rs708242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71464944	1.00[EUR][1000 genomes]
rs7305811	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7967350	0.91[AFR][1000 genomes]
rs7981004	0.81[ASW][hapmap]
rs833823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs833825	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs833830	0.81[ASW][hapmap]
rs833834	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs833835	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs863855	0.81[ASW][hapmap]
rs941193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs833829	TROAP	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49351400-49352400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:49351800-49352600	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:49351800-49358600	Weak transcription	Lung	lung
4	chr12:49351800-49365000	Weak transcription	Right Atrium	heart
5	chr12:49352000-49352400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:49352000-49352400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:49352000-49352400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:49352000-49352400	Enhancers	Primary B cells from cord blood	blood
9	chr12:49352000-49352400	Enhancers	Primary hematopoietic stem cells	blood
10	chr12:49352000-49352400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:49352000-49352400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:49352000-49352400	Active TSS	Brain Germinal Matrix	brain
13	chr12:49352000-49352400	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:49352000-49352400	Enhancers	Fetal Brain Male	brain
15	chr12:49352000-49352400	Enhancers	Fetal Intestine Large	intestine
16	chr12:49352000-49352400	Enhancers	Fetal Intestine Small	intestine
17	chr12:49352000-49352400	Enhancers	Fetal Kidney	kidney
18	chr12:49352000-49352400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr12:49352000-49352400	Enhancers	HMEC	breast
20	chr12:49352000-49352400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr12:49352000-49352600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr12:49352000-49354400	Weak transcription	HSMMtube	muscle
23	chr12:49352000-49354600	Weak transcription	HSMM	muscle
24	chr12:49352000-49354800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:49352000-49354800	Weak transcription	HUVEC	blood vessel
26	chr12:49352000-49355000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:49352000-49355000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:49352000-49355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:49352000-49355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:49352000-49355000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:49352000-49355200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:49352000-49355200	Weak transcription	NHDF-Ad	bronchial
33	chr12:49352200-49352400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:49352200-49352400	Enhancers	A549	lung
35	chr12:49352200-49352400	Enhancers	Dnd41	blood
36	chr12:49352200-49352400	Enhancers	Hela-S3	cervix
37	chr12:49352200-49355000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:49352200-49355200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:49352200-49355200	Weak transcription	NHEK	skin
40	chr12:49352200-49358400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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