Variant report

Variant	rs1038914
Chromosome Location	chr12:58011066-58011067
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
2	chr12:58009848..58012356-chr12:58118975..58121392,2	MCF-7	breast:
3	chr12:57913091..57915646-chr12:58010883..58013272,4	K562	blood:
4	chr12:57912181..57914315-chr12:58008996..58011925,2	MCF-7	breast:
5	chr12:53772778..53775585-chr12:58009878..58011429,2	MCF-7	breast:
6	chr12:57913428..57916180-chr12:58009743..58011363,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC26A10-1	chr12:58010567-58011071	NONHSAT028944

No data

Variant related genes	Relation type
ENSG00000135502	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000185591	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000224713	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1027315	0.92[ASN][1000 genomes]
rs1050045	0.90[JPT][hapmap]
rs1552842	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564374	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873919	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277324	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307095	0.94[ASN][1000 genomes]
rs2640610	0.85[ASN][1000 genomes]
rs34271193	0.81[ASN][1000 genomes]
rs7134861	0.81[ASN][1000 genomes]
rs7295422	0.90[JPT][hapmap]
rs7304145	0.89[ASN][1000 genomes]
rs7311632	0.90[JPT][hapmap]
rs7966795	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs799265	0.90[JPT][hapmap]
rs903067	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs923828	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1038914	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1038914	TENC1	cis	cerebellum	SCAN
rs1038914	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1038914	TSPAN31	cis	cerebellum	SCAN
rs1038914	MIP	cis	cerebellum	SCAN
rs1038914	OR6C4	cis	cerebellum	SCAN
rs1038914	FAM119B	cis	cerebellum	SCAN
rs1038914	FAM119B	cis	lymphoblastoid	seeQTL
rs1038914	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58011400	Weak transcription	Lung	lung
2	chr12:58005600-58013200	Weak transcription	Gastric	stomach
3	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
4	chr12:58006400-58011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
6	chr12:58006800-58011400	Strong transcription	Ovary	ovary
7	chr12:58006800-58011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:58006800-58011600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:58006800-58011600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:58006800-58011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:58006800-58012000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:58007000-58012000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:58007200-58011200	Strong transcription	Fetal Brain Female	brain
14	chr12:58008000-58011400	Strong transcription	Fetal Stomach	stomach
15	chr12:58008000-58012800	Weak transcription	HepG2	liver
16	chr12:58008400-58012000	Strong transcription	Aorta	Aorta
17	chr12:58009200-58011200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:58009200-58011800	Strong transcription	Colon Smooth Muscle	Colon
19	chr12:58009400-58012000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:58009800-58011800	Active TSS	Left Ventricle	heart
21	chr12:58010000-58011800	Active TSS	Right Atrium	heart
22	chr12:58010200-58013600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:58010400-58011200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:58010400-58011600	Weak transcription	Spleen	Spleen
25	chr12:58010400-58013600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:58010400-58014000	Weak transcription	Brain Substantia Nigra	brain
27	chr12:58010400-58014400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:58010600-58011400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:58010600-58012000	Enhancers	K562	blood
30	chr12:58010600-58012200	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:58010600-58013000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:58010600-58014000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:58010600-58014000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:58010600-58014200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:58010800-58011400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:58010800-58011600	Weak transcription	Brain Germinal Matrix	brain
37	chr12:58010800-58012000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:58010800-58013000	Weak transcription	Osteobl	bone
39	chr12:58010800-58013200	Weak transcription	Esophagus	oesophagus
40	chr12:58010800-58013600	Weak transcription	Brain Anterior Caudate	brain
41	chr12:58011000-58011200	Weak transcription	Fetal Lung	lung
42	chr12:58011000-58011600	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links