Variant report

Variant	rs9815819
Chromosome Location	chr3:112365127-112365128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112357844..112361438-chr3:112364098..112368101,7	MCF-7	breast:
2	chr3:112358518..112360693-chr3:112363292..112365603,2	K562	blood:
3	chr3:112362227..112366265-chr3:112408651..112412487,6	MCF-7	breast:
4	chr3:112364416..112367219-chr3:112696303..112699489,3	MCF-7	breast:
5	chr3:112364472..112367119-chr3:112708637..112711518,2	MCF-7	breast:
6	chr3:112361572..112365675-chr3:112707892..112711353,4	MCF-7	breast:
7	chr3:112363876..112366126-chr3:112709800..112712751,2	K562	blood:

Variant related genes	Relation type
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2279531	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3842905	0.92[YRI][hapmap]
rs6438086	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438087	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772337	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6794305	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs6807798	0.81[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs7611898	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620601	0.87[TSI][hapmap]
rs9683135	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9821100	0.85[CHD][hapmap]
rs9821338	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs9870933	0.89[TSI][hapmap]

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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9815819	BOC	cis	cerebellum	SCAN
rs9815819	ESAM	trans	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112358600-112365400	Weak transcription	Lung	lung
2	chr3:112359600-112365400	Weak transcription	Pancreas	Pancrea
3	chr3:112360800-112365200	Weak transcription	Psoas Muscle	Psoas
4	chr3:112360800-112365600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:112360800-112367800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:112361000-112365200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:112361000-112365800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112362200-112365200	Weak transcription	Placenta	Placenta
9	chr3:112362200-112365600	Weak transcription	Hela-S3	cervix
10	chr3:112362200-112366000	Weak transcription	Ovary	ovary
11	chr3:112362400-112365200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:112362400-112365400	Weak transcription	Fetal Heart	heart
13	chr3:112362400-112367600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:112362400-112367800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:112362600-112365200	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:112362800-112365200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:112362800-112365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:112362800-112365200	Enhancers	A549	lung
19	chr3:112362800-112365400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:112362800-112365400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:112362800-112365400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:112362800-112366800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:112362800-112367800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:112363000-112365200	Weak transcription	HMEC	breast
25	chr3:112363000-112365200	Weak transcription	NHEK	skin
26	chr3:112363000-112365400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:112363000-112365400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:112363000-112365400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:112363200-112365600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:112363400-112365200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:112363400-112365200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:112363400-112365200	Weak transcription	NHDF-Ad	bronchial
33	chr3:112363400-112365400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr3:112363400-112365400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:112363400-112373600	Weak transcription	Esophagus	oesophagus
36	chr3:112363600-112365200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:112363600-112365200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:112363600-112365200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:112363600-112365200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:112363600-112365400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:112363600-112365400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:112363600-112365400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:112363600-112365400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:112363600-112365400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:112363600-112365400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:112363600-112365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:112363600-112365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:112363600-112365600	Weak transcription	K562	blood
49	chr3:112363600-112365800	Weak transcription	Fetal Kidney	kidney
50	chr3:112363800-112365200	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links