Variant report

Variant	rs7486428
Chromosome Location	chr12:117411080-117411081
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	chr12:117409582..117412431-chr12:117414257..117415870,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10735100	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10735101	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10735102	0.86[ASW][hapmap]
rs10774895	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10774898	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10850730	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10850731	0.86[YRI][hapmap]
rs10850734	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10850742	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10850747	0.83[JPT][hapmap]
rs10850751	0.88[JPT][hapmap]
rs11068264	0.85[ASW][hapmap]
rs11068276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068292	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11834817	0.88[JPT][hapmap]
rs1472523	0.88[JPT][hapmap]
rs2062528	0.94[JPT][hapmap]
rs2173654	0.94[JPT][hapmap]
rs2291916	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2393113	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4562927	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs4766815	0.86[ASW][hapmap]
rs4766816	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4766823	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767474	0.86[ASW][hapmap]
rs4767477	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767484	0.86[ASW][hapmap]
rs4767486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767489	0.86[ASW][hapmap]
rs6490103	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490106	0.83[JPT][hapmap]
rs7133090	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297303	0.88[JPT][hapmap]
rs7302127	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs7487081	0.83[CEU][hapmap];0.88[MEX][hapmap]
rs7958680	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7962875	0.92[EUR][1000 genomes]
rs7964668	0.88[JPT][hapmap]
rs9634171	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7486428	HRK	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117384400-117411200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:117384600-117427400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:117387800-117463600	Weak transcription	HMEC	breast
5	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
6	chr12:117394600-117415400	Weak transcription	HSMMtube	muscle
7	chr12:117397000-117429200	Weak transcription	Right Ventricle	heart
8	chr12:117397000-117442400	Weak transcription	Colonic Mucosa	Colon
9	chr12:117398200-117417400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:117400400-117412000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:117400400-117417800	Weak transcription	K562	blood
12	chr12:117400800-117415400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:117402200-117417200	Weak transcription	Stomach Mucosa	stomach
14	chr12:117402600-117411200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:117403000-117412200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:117403400-117416800	Weak transcription	HUVEC	blood vessel
17	chr12:117403400-117418000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:117403400-117423200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:117403600-117413200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:117403600-117420400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:117404600-117427000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:117404600-117442400	Weak transcription	HepG2	liver
23	chr12:117404800-117426400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:117405400-117418000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr12:117405600-117420400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:117405600-117442400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:117408000-117420200	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:117408000-117427600	Weak transcription	Dnd41	blood
29	chr12:117408200-117411200	Weak transcription	Brain Anterior Caudate	brain
30	chr12:117408200-117417400	Weak transcription	Gastric	stomach
31	chr12:117408200-117424800	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:117408200-117426400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:117408200-117427000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:117408200-117429600	Weak transcription	Brain Substantia Nigra	brain
35	chr12:117408200-117442400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:117408400-117411200	Weak transcription	Brain Angular Gyrus	brain
37	chr12:117408400-117413400	Weak transcription	NH-A	brain
38	chr12:117408400-117420200	Weak transcription	Fetal Brain Male	brain
39	chr12:117408400-117420400	Weak transcription	Fetal Lung	lung
40	chr12:117408400-117432600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:117408400-117452200	Weak transcription	Thymus	Thymus
42	chr12:117408600-117415400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:117408600-117416400	Weak transcription	Brain Germinal Matrix	brain
44	chr12:117408600-117420800	Weak transcription	Fetal Heart	heart
45	chr12:117408600-117422400	Weak transcription	Fetal Intestine Small	intestine
46	chr12:117408800-117415400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:117409000-117427200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:117409200-117411600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:117409600-117412200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:117409800-117412000	Strong transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links