Variant report

Variant	rs1031477
Chromosome Location	chr12:50218644-50218645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr12:50218552-50220875	IMR90	lung:	n/a	chr12:50219337-50219352 chr12:50219050-50219059
2	POLR2A	chr12:50218506-50219040	HUVEC	blood vessel:	n/a	n/a
3	SPI1	chr12:50218605-50219529	HL-60	blood:	n/a	chr12:50219150-50219163 chr12:50219267-50219280

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50216203..50220741-chr12:50220862..50224448,8	MCF-7	breast:
2	chr12:50216965..50224421-chr12:50234869..50238255,17	MCF-7	breast:
3	chr12:50203774..50205961-chr12:50217957..50219971,2	K562	blood:
4	chr12:50197055..50201000-chr12:50217056..50221303,4	K562	blood:
5	chr12:50137650..50140394-chr12:50217891..50219857,2	MCF-7	breast:
6	chr12:50169257..50171499-chr12:50217406..50219140,2	MCF-7	breast:
7	chr12:50216445..50219303-chr12:50297052..50298599,2	K562	blood:
8	chr12:50181461..50183796-chr12:50216518..50220004,3	MCF-7	breast:
9	chr12:50133925..50140140-chr12:50217980..50223924,8	K562	blood:
10	chr12:50217971..50224800-chr12:50231213..50239207,27	MCF-7	breast:

No data

Variant related genes	Relation type
BCDIN3D-AS1	TF binding region
ENSG00000186666	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000258057	Chromatin interaction
ENSG00000135472	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1031476	0.82[EUR][1000 genomes]
rs10875976	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs11169162	0.83[ASW][hapmap];0.96[LWK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs11169166	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169167	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs11169170	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs4898534	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs4898535	0.90[ASN][1000 genomes]
rs55677077	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55758326	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66908137	0.82[EUR][1000 genomes]
rs7953539	0.93[ASN][1000 genomes]
rs7973894	0.89[CEU][hapmap];0.93[ASN][1000 genomes]
rs897054	0.80[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1031477	LALBA	cis	cerebellum	SCAN
rs1031477	DBX2	cis	parietal	SCAN
rs1031477	RPAP3	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50197600-50220400	Weak transcription	A549	lung
2	chr12:50200000-50219400	Weak transcription	Gastric	stomach
3	chr12:50203600-50219800	Weak transcription	Aorta	Aorta
4	chr12:50204400-50220200	Weak transcription	Fetal Kidney	kidney
5	chr12:50205200-50219000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:50205200-50220000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:50208800-50221200	Weak transcription	Small Intestine	intestine
8	chr12:50213600-50219000	Enhancers	Brain Hippocampus Middle	brain
9	chr12:50213600-50219000	Genic enhancers	Fetal Muscle Leg	muscle
10	chr12:50213800-50218800	Weak transcription	Hela-S3	cervix
11	chr12:50213800-50219000	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr12:50214400-50220200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:50214400-50220800	Enhancers	Placenta	Placenta
14	chr12:50215200-50221000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:50215400-50218800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:50215400-50219000	Weak transcription	Colonic Mucosa	Colon
17	chr12:50215400-50219200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:50215400-50219200	Weak transcription	Pancreas	Pancrea
19	chr12:50215400-50219600	Weak transcription	Liver	Liver
20	chr12:50215600-50218800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
21	chr12:50215800-50219000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:50215800-50219600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:50215800-50220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:50215800-50221200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:50216000-50218800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:50216000-50219000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:50216000-50220000	Weak transcription	Thymus	Thymus
28	chr12:50216000-50221000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:50216000-50221000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:50216200-50219200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:50216200-50220000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:50216200-50220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:50216200-50220800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:50216400-50219800	Weak transcription	Primary T cells from cord blood	blood
35	chr12:50216600-50220200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:50216800-50219400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:50216800-50219400	Enhancers	Left Ventricle	heart
38	chr12:50216800-50220600	Weak transcription	Psoas Muscle	Psoas
39	chr12:50217000-50219000	Enhancers	Right Atrium	heart
40	chr12:50217000-50219000	Enhancers	HepG2	liver
41	chr12:50217000-50220200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:50217200-50220000	Enhancers	Colon Smooth Muscle	Colon
43	chr12:50217200-50220400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:50217200-50221000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:50217400-50219200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:50217400-50219200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:50217400-50220600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:50217400-50220600	Enhancers	Duodenum Mucosa	Duodenum
49	chr12:50217600-50219000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:50217600-50220400	Enhancers	Fetal Heart	heart

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