Variant report

Variant	rs1470909
Chromosome Location	chr12:50183966-50183967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50183462..50185925-chr12:50186886..50188688,2	MCF-7	breast:
2	chr12:50178156..50180784-chr12:50182725..50184886,2	MCF-7	breast:
3	chr12:50183912..50186626-chr12:50222654..50225172,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1075366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1077498	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1077499	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10783320	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875969	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169161	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169162	0.83[TSI][hapmap]
rs2290442	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336448	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2603104	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2603107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603110	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2603111	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2603112	0.82[TSI][hapmap]
rs2720291	0.96[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2720296	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2720298	0.96[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2954129	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463912	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4898530	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729281	0.96[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7313400	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7313563	0.81[CEU][hapmap]
rs7488361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977112	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1470909	RAPGEF3	cis	parietal	SCAN
rs1470909	PLEKHA9	cis	cerebellum	SCAN
rs1470909	DBX2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50170000-50184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:50170200-50184400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:50170800-50191200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:50172400-50192600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:50172800-50184600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
8	chr12:50178200-50184400	Weak transcription	Aorta	Aorta
9	chr12:50178400-50184600	Weak transcription	Ovary	ovary
10	chr12:50178400-50194000	Weak transcription	NH-A	brain
11	chr12:50178400-50195000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:50178600-50184400	Weak transcription	Spleen	Spleen
13	chr12:50178600-50185600	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:50178800-50184400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:50178800-50184600	Weak transcription	Right Ventricle	heart
16	chr12:50178800-50185200	Weak transcription	Fetal Thymus	thymus
17	chr12:50178800-50191600	Weak transcription	NHDF-Ad	bronchial
18	chr12:50179000-50184400	Weak transcription	Lung	lung
19	chr12:50179000-50184600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
21	chr12:50179600-50195200	Weak transcription	Fetal Brain Male	brain
22	chr12:50180400-50189000	Weak transcription	NHEK	skin
23	chr12:50180600-50185000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:50181000-50184800	Weak transcription	Fetal Intestine Small	intestine
25	chr12:50181200-50184400	Weak transcription	Thymus	Thymus
26	chr12:50181600-50189200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:50181600-50190400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:50181800-50184400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:50181800-50184600	Weak transcription	Brain Anterior Caudate	brain
30	chr12:50181800-50185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:50181800-50188000	Weak transcription	Fetal Intestine Large	intestine
32	chr12:50181800-50190600	Weak transcription	A549	lung
33	chr12:50182000-50184000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:50182000-50189800	Weak transcription	Fetal Lung	lung
35	chr12:50182000-50191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:50182000-50191800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:50182200-50184400	Weak transcription	Brain Germinal Matrix	brain
38	chr12:50182200-50184400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:50182200-50184800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:50182200-50185200	Weak transcription	Gastric	stomach
41	chr12:50182200-50191200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:50182200-50191400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:50182400-50191000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr12:50183000-50188800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:50183000-50190400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:50183200-50185400	Strong transcription	Placenta	Placenta
47	chr12:50183200-50187600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:50183200-50197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links