Variant report

Variant	rs833823
Chromosome Location	chr12:49349856-49349857
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49210476..49213723-chr12:49348025..49351364,4	MCF-7	breast:
2	chr12:49349835..49352133-chr12:49390670..49393580,2	K562	blood:
3	chr12:49326822..49334011-chr12:49345841..49353556,12	MCF-7	breast:
4	chr12:49319039..49321186-chr12:49348048..49350961,2	MCF-7	breast:
5	chr12:49349202..49351999-chr12:49410599..49414055,4	MCF-7	breast:
6	chr12:49349007..49352698-chr12:49523718..49526243,3	K562	blood:
7	chr12:49349516..49351260-chr12:49410887..49413470,2	K562	blood:
8	chr12:49349745..49351260-chr12:49410630..49412387,2	K562	blood:
9	chr12:49317412..49320697-chr12:49349793..49352537,4	MCF-7	breast:
10	chr12:49244090..49248564-chr12:49349147..49352476,5	MCF-7	breast:
11	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
12	chr12:49258480..49261342-chr12:49348804..49351192,2	MCF-7	breast:
13	chr12:49349743..49353633-chr12:49353636..49360057,10	MCF-7	breast:
14	chr12:49348804..49352502-chr12:49411258..49414497,4	MCF-7	breast:
15	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:
16	chr12:49349770..49352703-chr12:49396550..49398736,3	K562	blood:
17	chr12:49349495..49352296-chr12:49353463..49356229,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255863	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000181418	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000134285	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000238395	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000169884	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11168810	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11610308	1.00[CHB][hapmap]
rs11833860	1.00[CHB][hapmap]
rs12122	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12318558	1.00[CHB][hapmap]
rs12424638	1.00[CHB][hapmap]
rs12829682	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2694841	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3741624	1.00[CHB][hapmap]
rs41291977	0.86[EUR][1000 genomes]
rs708242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71464944	1.00[EUR][1000 genomes]
rs7305811	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7967350	0.90[AFR][1000 genomes]
rs7981004	0.81[ASW][hapmap]
rs833825	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs833829	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]
rs833830	0.81[ASW][hapmap]
rs833834	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs833835	0.96[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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[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
rs833823	TROAP	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49347000-49350000	Weak transcription	Aorta	Aorta
2	chr12:49348000-49350000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:49348000-49350000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:49348000-49350200	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:49348000-49350800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr12:49348000-49352200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:49348400-49350000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr12:49348400-49351000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr12:49348600-49350000	Enhancers	Small Intestine	intestine
10	chr12:49348800-49350000	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr12:49348800-49350000	Flanking Active TSS	GM12878-XiMat	blood
12	chr12:49349000-49350000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:49349000-49350000	Enhancers	Stomach Mucosa	stomach
14	chr12:49349000-49350200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:49349000-49350200	Flanking Active TSS	Fetal Brain Female	brain
16	chr12:49349200-49350000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
17	chr12:49349200-49350000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:49349200-49350000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
19	chr12:49349200-49350000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:49349200-49350000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr12:49349200-49350000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:49349200-49350000	Flanking Active TSS	NH-A	brain
23	chr12:49349200-49352000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:49349400-49350000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
25	chr12:49349400-49350000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:49349400-49350000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:49349400-49350000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr12:49349400-49350000	Flanking Active TSS	NHDF-Ad	bronchial
29	chr12:49349400-49350000	Transcr. at gene 5' and 3'	NHEK	skin
30	chr12:49349400-49350000	Flanking Active TSS	NHLF	lung
31	chr12:49349400-49350200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
32	chr12:49349400-49350200	Enhancers	Primary T cells fromperipheralblood	blood
33	chr12:49349400-49350200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:49349400-49350200	Flanking Active TSS	Fetal Kidney	kidney
35	chr12:49349400-49350200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr12:49349400-49350200	Transcr. at gene 5' and 3'	A549	lung
37	chr12:49349400-49350200	Transcr. at gene 5' and 3'	K562	blood
38	chr12:49349400-49350400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr12:49349600-49350000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr12:49349600-49350000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:49349600-49350000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:49349600-49350000	Enhancers	Primary T cells from cord blood	blood
43	chr12:49349600-49350000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr12:49349600-49350000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:49349600-49350000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:49349600-49350000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:49349600-49350000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:49349600-49350000	Flanking Active TSS	Colonic Mucosa	Colon
49	chr12:49349600-49350000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:49349600-49350000	Transcr. at gene 5' and 3'	HSMM	muscle

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