Variant report

Variant	rs6794305
Chromosome Location	chr3:112355977-112355978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112354988..112357166-chr3:112709171..112711334,2	MCF-7	breast:
2	chr3:112279670..112281716-chr3:112353660..112356312,2	MCF-7	breast:
3	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2279531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3842905	0.80[EUR][1000 genomes]
rs6438086	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6438087	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6807798	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611898	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9683135	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9815819	0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs9821338	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.82[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6794305	BOC	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112342600-112359600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112343400-112358000	Weak transcription	Pancreas	Pancrea
3	chr3:112345200-112359400	Weak transcription	Esophagus	oesophagus
4	chr3:112348200-112358400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:112348600-112357200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:112348800-112358400	Weak transcription	Hela-S3	cervix
7	chr3:112351400-112358600	Transcr. at gene 5' and 3'	Osteobl	bone
8	chr3:112351800-112357800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:112352000-112356000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:112352600-112358400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:112353000-112358600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:112353000-112358600	Weak transcription	Fetal Brain Male	brain
13	chr3:112353400-112356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:112353800-112356400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:112353800-112357200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:112354000-112356200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:112354000-112356600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:112354000-112357000	Active TSS	Brain Hippocampus Middle	brain
19	chr3:112354000-112359000	Flanking Active TSS	NH-A	brain
20	chr3:112354000-112359200	Weak transcription	Fetal Brain Female	brain
21	chr3:112354000-112360600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:112354200-112356000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:112354200-112357800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:112354200-112358000	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr3:112354200-112358200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:112354400-112356200	Weak transcription	Fetal Intestine Large	intestine
27	chr3:112354400-112356800	Active TSS	NHLF	lung
28	chr3:112354400-112357800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:112354400-112357800	Active TSS	HSMMtube	muscle
30	chr3:112354400-112359000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:112354600-112356000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:112354600-112359400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:112354800-112356000	Flanking Active TSS	Fetal Stomach	stomach
34	chr3:112354800-112356400	Active TSS	Placenta Amnion	Placenta Amnion
35	chr3:112354800-112356600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:112354800-112356600	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr3:112354800-112357200	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:112354800-112357600	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr3:112354800-112358600	Weak transcription	NHEK	skin
40	chr3:112354800-112359000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:112354800-112359000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:112354800-112359000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:112354800-112360000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:112355000-112358600	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr3:112355000-112358800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:112355000-112359000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:112355200-112356600	Active TSS	A549	lung
48	chr3:112355200-112357000	Active TSS	Right Atrium	heart
49	chr3:112355200-112358400	Weak transcription	HUVEC	blood vessel
50	chr3:112355400-112356600	Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links