Variant report

Variant	rs12945908
Chromosome Location	chr17:67258921-67258922
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	chr17:67257444..67260206-chr17:67267732..67269539,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1011549	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10445224	0.84[ASN][1000 genomes]
rs10491177	0.83[AMR][1000 genomes]
rs11077445	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11649744	0.81[ASN][1000 genomes]
rs11650955	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11651815	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11651872	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11652207	0.81[ASN][1000 genomes]
rs11654323	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11656389	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869324	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11871771	0.82[AMR][1000 genomes]
rs12449649	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12450167	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12450402	0.81[AMR][1000 genomes]
rs12450522	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12450743	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12452340	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12937191	0.85[AMR][1000 genomes]
rs12937947	0.81[AMR][1000 genomes]
rs12938039	0.85[AMR][1000 genomes]
rs12938064	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12938097	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12941297	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12942763	0.82[AMR][1000 genomes]
rs12942867	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12943504	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12944980	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12945481	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12946566	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12946776	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12952942	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1550828	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1558168	0.82[ASN][1000 genomes]
rs15886	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2364996	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34334829	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34609440	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34985085	0.81[ASN][1000 genomes]
rs4310935	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4310936	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs471193	0.81[ASN][1000 genomes]
rs557491	0.86[ASN][1000 genomes]
rs55773491	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57949169	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs817121	0.80[ASN][1000 genomes]
rs817128	0.80[ASN][1000 genomes]
rs9646388	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv1055156	chr17:67239695-67272311	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a
5	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	esv275054	chr17:67256226-67260145	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12945908	ABCA9	cis	intralobular white matter	BrainEAC

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67230600-67259600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr17:67230800-67271800	Weak transcription	Pancreas	Pancrea
3	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:67236000-67283000	Weak transcription	Ovary	ovary
5	chr17:67236400-67278000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:67236800-67280800	Weak transcription	Brain Angular Gyrus	brain
7	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
8	chr17:67238800-67278000	Weak transcription	Thymus	Thymus
9	chr17:67239200-67262400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:67240000-67289200	Weak transcription	Esophagus	oesophagus
11	chr17:67240000-67296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:67242000-67260600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:67242000-67265000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr17:67242200-67265000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:67242200-67265000	Weak transcription	NHEK	skin
16	chr17:67242400-67289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:67243000-67264800	Weak transcription	NHDF-Ad	bronchial
18	chr17:67243600-67305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:67244000-67262400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
21	chr17:67245600-67261600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr17:67245800-67278000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:67248000-67284400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr17:67249000-67264600	Weak transcription	Left Ventricle	heart
25	chr17:67249000-67278400	Weak transcription	Fetal Intestine Small	intestine
26	chr17:67250000-67289200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:67250200-67280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr17:67250800-67264600	Weak transcription	Osteobl	bone
29	chr17:67250800-67265200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:67250800-67277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:67251200-67279000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr17:67251400-67260000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr17:67251400-67264000	Weak transcription	HUVEC	blood vessel
34	chr17:67251400-67264200	Weak transcription	Fetal Intestine Large	intestine
35	chr17:67251400-67264200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr17:67251400-67272000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:67251400-67273000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr17:67251400-67277600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr17:67251400-67277800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr17:67251400-67278000	Weak transcription	Primary T cells from cord blood	blood
41	chr17:67251600-67265800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr17:67251600-67265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:67251600-67274000	Weak transcription	GM12878-XiMat	blood
44	chr17:67251600-67278200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr17:67251600-67289200	Weak transcription	Brain Anterior Caudate	brain
46	chr17:67251800-67264600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:67251800-67264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr17:67252000-67259600	Weak transcription	Liver	Liver
49	chr17:67252200-67264600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:67252400-67272400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links