Variant report

Variant	rs3751052
Chromosome Location	chr11:9072140-9072141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:9072078-9072213	HepG2	liver:	n/a	n/a
2	MAFK	chr11:9072075-9072343	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9070098..9074605-chr11:9077166..9080417,4	K562	blood:
2	chr11:9072036..9074888-chr11:9076818..9079933,4	K562	blood:

Variant related genes	Relation type
SCUBE2	TF binding region
ENSG00000253973	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7106593	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7124953	0.82[YRI][hapmap]
rs7126825	0.83[YRI][hapmap]

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	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	nsv467704	chr11:9059192-9125301	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv553454	chr11:9059192-9125301	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3751052	LMO1	cis	cerebellum	SCAN
rs3751052	RRP8	cis	parietal	SCAN
rs3751052	OR52A5	cis	cerebellum	SCAN
rs3751052	RPL27A	cis	parietal	SCAN
rs3751052	NRIP3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9058400-9099800	Weak transcription	Aorta	Aorta
2	chr11:9059200-9074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:9065600-9073400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:9066000-9081800	Weak transcription	Small Intestine	intestine
5	chr11:9067600-9072200	Enhancers	Fetal Muscle Leg	muscle
6	chr11:9069000-9080400	Weak transcription	Fetal Intestine Large	intestine
7	chr11:9069000-9092400	Weak transcription	Fetal Intestine Small	intestine
8	chr11:9069200-9074600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:9069200-9083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:9070200-9078600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:9070200-9087400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:9070200-9097200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:9070400-9072200	Enhancers	Fetal Lung	lung
14	chr11:9070400-9074000	Weak transcription	Pancreas	Pancrea
15	chr11:9070400-9075200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr11:9070400-9077600	Weak transcription	Adipose Nuclei	Adipose
17	chr11:9070400-9078000	Weak transcription	Gastric	stomach
18	chr11:9070400-9098400	Weak transcription	Colonic Mucosa	Colon
19	chr11:9070600-9075000	Weak transcription	NHDF-Ad	bronchial
20	chr11:9070600-9077400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:9070600-9087800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:9070600-9091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:9071200-9072800	Weak transcription	Placenta	Placenta
24	chr11:9071200-9076800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr11:9071200-9077800	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:9071200-9087200	Weak transcription	Fetal Brain Male	brain
27	chr11:9072000-9072200	Enhancers	Fetal Muscle Trunk	muscle
28	chr11:9072000-9074600	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links