Variant report

Variant	rs10880939
Chromosome Location	chr12:46614641-46614642
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46613955..46615802-chr12:46659789..46661302,2	MCF-7	breast:
2	chr12:46611489..46616057-chr12:46626284..46631509,6	MCF-7	breast:
3	chr12:46611672..46615140-chr12:46658386..46664443,5	K562	blood:
4	chr12:46597858..46599601-chr12:46614567..46617452,2	MCF-7	breast:
5	chr12:46611743..46615456-chr12:46661323..46664567,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs4768108	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7970176	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979828	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880939	SLC48A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:46596000-46618200	Weak transcription	Aorta	Aorta
3	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
4	chr12:46604000-46623400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:46604000-46633800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:46604000-46637400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:46604400-46618600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:46605000-46615000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:46605000-46615200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:46607000-46615000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:46608400-46615000	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:46608400-46618200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:46609200-46618600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr12:46610200-46619000	Weak transcription	Psoas Muscle	Psoas
15	chr12:46610400-46624000	Weak transcription	Pancreas	Pancrea
16	chr12:46610600-46640000	Weak transcription	Esophagus	oesophagus
17	chr12:46611400-46615800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:46611600-46616800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:46612000-46615400	Strong transcription	Fetal Muscle Leg	muscle
20	chr12:46612000-46617200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:46612200-46615200	Enhancers	Fetal Intestine Small	intestine
22	chr12:46612200-46615200	Enhancers	Small Intestine	intestine
23	chr12:46612200-46616000	Enhancers	Placenta	Placenta
24	chr12:46612200-46618200	Genic enhancers	NHEK	skin
25	chr12:46612400-46615400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:46612400-46618400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:46612600-46618400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:46613000-46616800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:46613200-46615400	Enhancers	HSMM	muscle
30	chr12:46613200-46615800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:46613200-46616000	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr12:46613200-46616200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:46613200-46616400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
34	chr12:46613200-46616400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
35	chr12:46613200-46617200	Genic enhancers	Hela-S3	cervix
36	chr12:46613200-46617400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:46613200-46618800	Strong transcription	HepG2	liver
38	chr12:46613200-46619200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr12:46613200-46619600	Enhancers	Colon Smooth Muscle	Colon
40	chr12:46613200-46619800	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr12:46613400-46614800	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:46613400-46615000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:46613400-46615000	Enhancers	HSMMtube	muscle
44	chr12:46613400-46615000	Enhancers	Osteobl	bone
45	chr12:46613400-46615600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:46613400-46615800	Enhancers	Brain Hippocampus Middle	brain
47	chr12:46613400-46615800	Enhancers	Brain Substantia Nigra	brain
48	chr12:46613400-46615800	Flanking Active TSS	HUVEC	blood vessel
49	chr12:46613400-46616000	Enhancers	Stomach Smooth Muscle	stomach
50	chr12:46613400-46616400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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