Variant report

Variant	rs11174554
Chromosome Location	chr12:62969668-62969669
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:6)
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	CEBPB	chr12:62969530-62969785	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:62959063..62961641-chr12:62967844..62970820,2	K562	blood:
2	chr12:62967790..62972054-chr12:63185896..63188649,3	MCF-7	breast:
3	chr12:62962682..62964507-chr12:62967795..62969952,2	K562	blood:
4	chr12:62952906..62954502-chr12:62968020..62970185,2	K562	blood:
5	chr12:62964193..62966992-chr12:62967473..62969692,2	MCF-7	breast:
6	chr12:62968394..62971296-chr12:62995438..62997947,2	MCF-7	breast:

No data

Variant related genes	Relation type
MON2	TF binding region
ENSG00000221949	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000061987	Chromatin interaction
ENSG00000199179	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10877892	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10877903	0.82[JPT][hapmap]
rs11174456	0.87[CHD][hapmap];0.83[GIH][hapmap]
rs11174491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11174502	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174503	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174515	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174526	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11174531	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174558	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174560	0.93[EUR][1000 genomes]
rs11174561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11174566	0.93[EUR][1000 genomes]
rs11174567	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174592	1.00[JPT][hapmap]
rs11559995	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12161814	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12228446	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12229932	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17098035	0.84[MKK][hapmap]
rs3825305	0.89[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs4405369	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4494347	0.87[EUR][1000 genomes]
rs7302781	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74095806	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74095822	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953138	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11174554	NDUFA4L2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:62915800-62971600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
4	chr12:62919800-62970000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:62924400-62969800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:62938000-62995400	Weak transcription	Stomach Mucosa	stomach
8	chr12:62944600-62989000	Weak transcription	Colonic Mucosa	Colon
9	chr12:62950400-62995600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:62950600-62975000	Weak transcription	Right Ventricle	heart
11	chr12:62950600-62982600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:62950600-62991200	Weak transcription	Gastric	stomach
13	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
14	chr12:62950800-62987600	Weak transcription	Pancreas	Pancrea
15	chr12:62950800-62995000	Weak transcription	NHEK	skin
16	chr12:62951000-62987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:62951200-62971600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:62951200-62979600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:62951200-62986800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:62951200-62988600	Weak transcription	Spleen	Spleen
22	chr12:62951200-62995200	Weak transcription	Hela-S3	cervix
23	chr12:62951200-62995600	Weak transcription	HSMMtube	muscle
24	chr12:62951400-62995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:62953400-62996000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:62954800-62989000	Weak transcription	Lung	lung
27	chr12:62954800-62995600	Weak transcription	Brain Anterior Caudate	brain
28	chr12:62955000-62987800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:62955200-62995200	Weak transcription	HepG2	liver
30	chr12:62955600-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:62957000-62995600	Weak transcription	Fetal Brain Male	brain
32	chr12:62957200-62972400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:62957200-62995600	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:62958600-62970000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:62958600-62970400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:62958600-62972800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:62958600-62972800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:62958800-62970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:62959400-62979800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:62959600-62995600	Weak transcription	NHLF	lung
41	chr12:62960000-62979600	Weak transcription	K562	blood
42	chr12:62960000-62982800	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:62961200-62995600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:62961400-62971400	Weak transcription	A549	lung
45	chr12:62961400-62982600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:62961400-62989200	Weak transcription	Psoas Muscle	Psoas
47	chr12:62961400-62995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:62961400-62995600	Weak transcription	Brain Germinal Matrix	brain
49	chr12:62961600-62995600	Weak transcription	Fetal Brain Female	brain
50	chr12:62961800-62969800	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links