Variant report

Variant	rs1679372
Chromosome Location	chr12:75905165-75905166
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75895269..75897744-chr12:75903455..75905180,2	MCF-7	breast:
2	chr12:75897120..75901453-chr12:75903276..75905265,4	MCF-7	breast:
3	chr12:75722764..75725346-chr12:75903212..75905334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111615	Chromatin interaction
ENSG00000180881	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1108515	0.87[YRI][hapmap]
rs1275477	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1679375	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1679376	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1679377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1697751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17115358	0.87[YRI][hapmap]
rs1909976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2652020	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3864889	0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3952736	1.00[MEX][hapmap]
rs4019401	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7979374	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1679372	C10orf108	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75903200-75906000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr12:75903400-75906000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:75903800-75905200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:75903800-75905600	Active TSS	GM12878-XiMat	blood
5	chr12:75903800-75906000	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:75903800-75906200	Active TSS	A549	lung
7	chr12:75904000-75905400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:75904000-75905600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:75904000-75905600	Active TSS	K562	blood
10	chr12:75904000-75905800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:75904000-75905800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:75904000-75905800	Active TSS	Aorta	Aorta
13	chr12:75904000-75905800	Active TSS	Fetal Intestine Large	intestine
14	chr12:75904000-75906000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr12:75904000-75906000	Active TSS	Psoas Muscle	Psoas
16	chr12:75904200-75905200	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:75904200-75905600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr12:75904200-75905600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:75904200-75905600	Active TSS	HMEC	breast
20	chr12:75904200-75905800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:75904200-75905800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:75904200-75905800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:75904200-75905800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:75904200-75905800	Active TSS	Ovary	ovary
25	chr12:75904200-75905800	Active TSS	Right Ventricle	heart
26	chr12:75904200-75905800	Active TSS	NHDF-Ad	bronchial
27	chr12:75904200-75906000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr12:75904200-75906000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:75904200-75906000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:75904200-75906000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr12:75904200-75906000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:75904200-75906000	Active TSS	Fetal Thymus	thymus
33	chr12:75904200-75906000	Active TSS	Right Atrium	heart
34	chr12:75904200-75906000	Active TSS	NH-A	brain
35	chr12:75904400-75905400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:75904400-75905400	Active TSS	NHEK	skin
37	chr12:75904400-75905600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:75904400-75905600	Active TSS	Placenta	Placenta
39	chr12:75904400-75905600	Active TSS	HSMM	muscle
40	chr12:75904400-75905800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr12:75904400-75905800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:75904400-75905800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:75904400-75905800	Active TSS	Fetal Muscle Trunk	muscle
44	chr12:75904400-75906000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:75904400-75906000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:75904400-75906000	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr12:75904400-75906000	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr12:75904400-75906000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr12:75904400-75906000	Active TSS	Fetal Muscle Leg	muscle
50	chr12:75904400-75906000	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links