Variant report

Variant	rs11615499
Chromosome Location	chr12:63200121-63200122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62994530..62996807-chr12:63199626..63201267,3	MCF-7	breast:
2	chr12:63199599..63203021-chr12:63327294..63329908,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111110	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000252660	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10506448	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10506449	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10506450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs10877914	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877917	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877918	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877919	0.83[ASN][1000 genomes]
rs10877920	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs11174650	1.00[GIH][hapmap]
rs11174655	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174656	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174657	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174658	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174659	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174660	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174661	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174662	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174664	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174665	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174666	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174667	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174669	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174677	0.88[ASN][1000 genomes]
rs11174678	0.88[ASN][1000 genomes]
rs11174681	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11174682	0.83[ASN][1000 genomes]
rs11174684	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11174689	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11495591	0.86[ASN][1000 genomes]
rs12367672	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12369052	0.83[ASN][1000 genomes]
rs12371724	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17120377	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs17735307	1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1908185	0.86[ASN][1000 genomes]
rs337516	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337517	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3912983	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4378444	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58709968	0.83[AFR][1000 genomes]
rs7132872	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7311601	1.00[YRI][hapmap]
rs73130065	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73130066	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73130069	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130081	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73130084	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73130086	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73130088	0.88[ASN][1000 genomes]
rs73130089	0.88[ASN][1000 genomes]
rs73135674	0.81[ASN][1000 genomes]
rs73135684	0.83[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	nsv899160	chr12:63149213-63209623	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11615499	FAM119B	cis	parietal	SCAN
rs11615499	DCTN2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63175200-63206800	Weak transcription	Pancreas	Pancrea
2	chr12:63181200-63200400	Weak transcription	Lung	lung
3	chr12:63187800-63205200	Weak transcription	K562	blood
4	chr12:63187800-63206400	Weak transcription	Osteobl	bone
5	chr12:63187800-63206800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:63187800-63211400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:63188000-63206800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:63192800-63211400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:63193000-63201400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:63193400-63206800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:63195400-63206000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:63195600-63211400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:63195600-63211400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:63195800-63228600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:63196000-63201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:63196000-63206600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:63196000-63206800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:63196000-63206800	Weak transcription	Fetal Intestine Large	intestine
19	chr12:63196000-63206800	Weak transcription	Right Ventricle	heart
20	chr12:63196000-63213600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:63196000-63213800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:63196000-63225800	Weak transcription	Gastric	stomach
23	chr12:63196400-63201400	Weak transcription	HepG2	liver
24	chr12:63196400-63213600	Weak transcription	Fetal Intestine Small	intestine
25	chr12:63197400-63206600	Weak transcription	Brain Angular Gyrus	brain
26	chr12:63198000-63206000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:63198000-63206600	Weak transcription	Brain Substantia Nigra	brain
28	chr12:63199200-63206600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:63199400-63201400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:63200000-63201000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links