Variant report

Variant	rs699568
Chromosome Location	chr12:63271170-63271171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:63270778..63274570-chr12:63326968..63330473,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252660	Chromatin interaction
ENSG00000111110	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11174704	0.88[CEU][hapmap]
rs2594711	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839798	0.93[CHD][hapmap]
rs479356	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs481867	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs482794	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs540694	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs572873	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs575657	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599969	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs629499	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs669622	0.80[ASN][1000 genomes]
rs688624	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs699567	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs771973	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs699568	MON2	cis	parietal	SCAN
rs699568	C12orf61	cis	parietal	SCAN
rs699568	FAM183A	trans	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63258200-63277200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:63260200-63275400	Weak transcription	Pancreas	Pancrea
3	chr12:63260800-63275200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:63261200-63275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:63261200-63277800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:63262400-63275200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:63262400-63277000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:63262800-63276000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:63263400-63277200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:63267400-63277600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:63267800-63274200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:63268000-63285000	Weak transcription	Fetal Intestine Large	intestine
13	chr12:63268200-63272400	Weak transcription	Placenta	Placenta
14	chr12:63268200-63274400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:63268400-63273200	Strong transcription	HepG2	liver
16	chr12:63268600-63280600	Weak transcription	Brain Anterior Caudate	brain
17	chr12:63269600-63271400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr12:63269600-63271800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:63269800-63271400	Enhancers	Brain Hippocampus Middle	brain
20	chr12:63270000-63271200	Enhancers	Brain Angular Gyrus	brain
21	chr12:63270000-63271200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:63270200-63273600	Weak transcription	Osteobl	bone
23	chr12:63270400-63271200	Enhancers	Left Ventricle	heart
24	chr12:63270400-63271200	Enhancers	Right Atrium	heart
25	chr12:63270600-63271200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:63270600-63271200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:63270600-63275200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:63270800-63271200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:63270800-63271400	Enhancers	Brain Substantia Nigra	brain
30	chr12:63270800-63271600	Enhancers	Brain Cingulate Gyrus	brain
31	chr12:63271000-63271200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr12:63271000-63271200	Weak transcription	Aorta	Aorta
33	chr12:63271000-63271200	Flanking Active TSS	Ovary	ovary
34	chr12:63271000-63271600	Enhancers	Fetal Muscle Leg	muscle
35	chr12:63271000-63271800	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links