Variant report

Variant	rs11169270
Chromosome Location	chr12:50483032-50483033
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50482709..50484515-chr12:50550134..50551963,2	K562	blood:
2	chr12:50475132..50479699-chr12:50479828..50484275,5	K562	blood:
3	chr12:50478595..50483647-chr12:50502911..50507517,7	K562	blood:
4	chr12:50482430..50484025-chr12:50560178..50562412,2	K562	blood:
5	chr12:50478759..50480659-chr12:50481009..50483998,3	K562	blood:
6	chr12:50481586..50483446-chr12:50561055..50562611,2	MCF-7	breast:
7	chr12:50475972..50484033-chr12:50500850..50507517,14	K562	blood:
8	chr12:50482709..50485025-chr12:50550134..50552131,3	K562	blood:
9	chr12:50477567..50484756-chr12:50559008..50565131,16	MCF-7	breast:
10	chr12:50468886..50470594-chr12:50481318..50483189,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139624	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000066117	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10875995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875996	0.88[EUR][1000 genomes]
rs11169263	0.89[MEX][hapmap]
rs11169282	0.80[GIH][hapmap]
rs1554844	0.80[GIH][hapmap]
rs17124432	0.80[GIH][hapmap]
rs17124559	1.00[LWK][hapmap]
rs3184122	1.00[CHD][hapmap]
rs3736309	1.00[LWK][hapmap]
rs3741562	0.80[GIH][hapmap]
rs376184	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs4898546	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs56990521	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590460	0.92[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs706794	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs7294618	0.80[GIH][hapmap]
rs7307230	0.80[GIH][hapmap]
rs73299515	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73299518	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956491	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961065	0.80[GIH][hapmap]
rs7961112	0.80[GIH][hapmap]
rs7964698	0.83[ASN][1000 genomes]
rs836175	0.82[EUR][1000 genomes]
rs836178	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11169270	LASS5	cis	cerebellum	SCAN
rs11169270	SLC38A1	cis	parietal	SCAN
rs11169270	AQP6	cis	parietal	SCAN
rs11169270	SNORA2A	cis	parietal	SCAN
rs11169270	LASS5	cis	multi-tissue	Pritchard
rs11169270	ATF1	cis	parietal	SCAN
rs11169270	LASS5	cis	parietal	SCAN
rs11169270	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50479800-50488200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:50480000-50483600	Weak transcription	Right Ventricle	heart
3	chr12:50480000-50485400	Weak transcription	Stomach Mucosa	stomach
4	chr12:50480000-50486000	Strong transcription	Colon Smooth Muscle	Colon
5	chr12:50480000-50494800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr12:50480000-50496400	Weak transcription	Right Atrium	heart
7	chr12:50480200-50484200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:50480200-50484800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:50480200-50489400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:50480200-50494800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:50480200-50494800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:50480200-50496200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:50480200-50496600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:50480200-50496600	Strong transcription	Thymus	Thymus
15	chr12:50480200-50496800	Strong transcription	Fetal Stomach	stomach
16	chr12:50480400-50483200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:50480400-50486400	Strong transcription	K562	blood
18	chr12:50480400-50493800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:50480400-50494400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr12:50480400-50494400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:50480400-50494600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:50480400-50494800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:50480400-50494800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:50480400-50494800	Strong transcription	Fetal Intestine Large	intestine
25	chr12:50480400-50494800	Strong transcription	Placenta	Placenta
26	chr12:50480400-50495600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:50480400-50495800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:50480400-50496000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:50480400-50496200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:50480400-50496200	Strong transcription	A549	lung
31	chr12:50480400-50496600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:50480400-50496600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:50480400-50496600	Strong transcription	Primary T cells from cord blood	blood
34	chr12:50480400-50496600	Strong transcription	Fetal Lung	lung
35	chr12:50480600-50483200	Genic enhancers	NHDF-Ad	bronchial
36	chr12:50480600-50483400	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr12:50480600-50486000	Strong transcription	Rectal Smooth Muscle	rectum
38	chr12:50480600-50491000	Strong transcription	Hela-S3	cervix
39	chr12:50480600-50492200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:50480600-50493200	Strong transcription	Adipose Nuclei	Adipose
41	chr12:50480600-50493600	Strong transcription	HSMMtube	muscle
42	chr12:50480600-50494000	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr12:50480600-50494600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:50480600-50494600	Strong transcription	Left Ventricle	heart
45	chr12:50480600-50494800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:50480600-50494800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:50480600-50495000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:50480600-50495000	Strong transcription	Spleen	Spleen
49	chr12:50480600-50495400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:50480600-50495800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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