Variant report

Variant	rs2272391
Chromosome Location	chr12:50471630-50471631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:
2	chr12:50471491..50474468-chr12:50505629..50507284,2	K562	blood:
3	chr12:50465226..50467523-chr12:50469793..50471990,2	K562	blood:

Variant related genes	Relation type
ENSG00000110881	Chromatin interaction
ENSG00000066117	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000272368	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1044370	0.88[CEU][hapmap]
rs1979702	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3782323	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs578470	0.85[EUR][1000 genomes]
rs646782	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs706790	0.87[EUR][1000 genomes]
rs706791	0.92[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs706792	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs706793	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs7139363	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7305558	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs835592	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs836172	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs836177	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs836188	0.87[EUR][1000 genomes]
rs836189	0.87[EUR][1000 genomes]
rs844347	0.92[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs860698	0.96[CEU][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2272391	CERS5	cis	Nerve Tibial	GTEx
rs2272391	SNORA2A	cis	parietal	SCAN
rs2272391	LASS5	cis	multi-tissue	Pritchard
rs2272391	LASS5	cis	cerebellum	SCAN
rs2272391	SLC38A1	cis	parietal	SCAN
rs2272391	TMEM106C	cis	cerebellum	SCAN
rs2272391	LASS5	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
3	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
4	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:50464800-50478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:50464800-50478200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:50466200-50472200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:50466800-50474800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:50469400-50473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:50469400-50474400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:50469400-50474800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:50469400-50474800	Weak transcription	Right Ventricle	heart
15	chr12:50469400-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:50469400-50478200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:50469400-50478200	Weak transcription	Fetal Brain Male	brain
18	chr12:50469600-50471800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:50469600-50474400	Weak transcription	K562	blood
20	chr12:50469600-50474600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:50469600-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:50469600-50477000	Strong transcription	Fetal Brain Female	brain
23	chr12:50469600-50477600	Weak transcription	HMEC	breast
24	chr12:50469600-50478200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:50469600-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:50469600-50478200	Weak transcription	Brain Angular Gyrus	brain
27	chr12:50469600-50478200	Weak transcription	Brain Anterior Caudate	brain
28	chr12:50469600-50478200	Weak transcription	Fetal Lung	lung
29	chr12:50469600-50478200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:50469800-50472000	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:50469800-50473600	Weak transcription	Fetal Intestine Small	intestine
32	chr12:50469800-50476000	Weak transcription	Colonic Mucosa	Colon
33	chr12:50469800-50478200	Weak transcription	Gastric	stomach
34	chr12:50470000-50473400	Weak transcription	Fetal Intestine Large	intestine
35	chr12:50470000-50473400	Weak transcription	HepG2	liver
36	chr12:50470000-50478200	Weak transcription	Liver	Liver
37	chr12:50470600-50474600	Strong transcription	Fetal Stomach	stomach
38	chr12:50471200-50474000	Strong transcription	Brain Hippocampus Middle	brain
39	chr12:50471200-50476200	Strong transcription	Brain Germinal Matrix	brain
40	chr12:50471400-50471800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:50471400-50477600	Weak transcription	GM12878-XiMat	blood
42	chr12:50471600-50472600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:50471600-50474800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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