Variant report

Variant	rs9668292
Chromosome Location	chr12:49186296-49186297
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49185219..49191305-chr12:49206326..49211471,6	MCF-7	breast:
2	chr12:49180478..49186692-chr12:49206898..49214052,14	MCF-7	breast:
3	chr12:49185540..49187110-chr12:49199114..49201849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10875874	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875875	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168732	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11168733	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11168734	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168736	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168737	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168738	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168739	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168740	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168742	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12306165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12307769	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12314663	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468640	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35801460	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729969	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs3729980	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3730069	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3730070	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3730072	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3730074	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs68003719	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132180	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7300155	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs7307701	0.86[ASN][1000 genomes]
rs7975385	1.00[CHD][hapmap]
rs9804777	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9668292	ARID2	cis	parietal	SCAN
rs9668292	RAPGEF3	cis	parietal	SCAN
rs9668292	CACNB3	cis	parietal	SCAN
rs9668292	CACNB3	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49183200-49188400	Weak transcription	NHEK	skin
2	chr12:49183800-49188400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:49183800-49190000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:49184000-49188200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:49184000-49188400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:49184000-49188400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:49184000-49188600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:49184000-49188800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:49184000-49189600	Weak transcription	Adipose Nuclei	Adipose
10	chr12:49184200-49187200	Weak transcription	Placenta	Placenta
11	chr12:49184200-49187400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:49184200-49188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:49184200-49188200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:49184200-49188600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:49184200-49188600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:49184200-49188600	Weak transcription	HMEC	breast
17	chr12:49184200-49188800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:49184200-49188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:49184200-49189200	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:49184200-49189400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:49184200-49189600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:49184200-49189600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:49184200-49189600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:49184200-49189600	Weak transcription	Esophagus	oesophagus
25	chr12:49184200-49193800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:49184200-49194400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:49184200-49198800	Weak transcription	NHLF	lung
28	chr12:49184400-49188200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:49184400-49188600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:49184400-49188600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:49184400-49188600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:49184400-49188600	Weak transcription	Fetal Kidney	kidney
33	chr12:49184400-49188600	Weak transcription	Stomach Mucosa	stomach
34	chr12:49184400-49188600	Weak transcription	A549	lung
35	chr12:49184400-49188600	Weak transcription	Hela-S3	cervix
36	chr12:49184400-49188600	Weak transcription	HepG2	liver
37	chr12:49184400-49188800	Weak transcription	Fetal Heart	heart
38	chr12:49184400-49189200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:49184400-49189200	Weak transcription	Liver	Liver
40	chr12:49184400-49189800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:49184400-49194000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:49184800-49188400	Weak transcription	Fetal Intestine Small	intestine
43	chr12:49185600-49189000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:49185800-49186400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr12:49186200-49186400	Enhancers	Colonic Mucosa	Colon
46	chr12:49186200-49186800	Enhancers	Fetal Intestine Large	intestine
47	chr12:49186200-49188800	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links