Variant report

Variant	rs11713226
Chromosome Location	chr3:140970556-140970557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140949417..140951197-chr3:140969315..140971449,2	MCF-7	breast:
2	chr3:140960166..140963166-chr3:140967948..140970939,3	MCF-7	breast:
3	chr3:140962275..140965128-chr3:140970545..140973245,4	K562	blood:
4	chr3:140966619..140969493-chr3:140970424..140973132,3	MCF-7	breast:
5	chr3:140969628..140971138-chr3:140978622..140980920,2	K562	blood:
6	chr3:140968757..140971307-chr3:140972187..140974906,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11556022	1.00[JPT][hapmap]
rs11710222	0.84[ASN][1000 genomes]
rs11713257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11921252	0.82[CEU][hapmap]
rs16851191	0.89[CEU][hapmap];0.84[ASN][1000 genomes]
rs16851272	0.83[CEU][hapmap]
rs3796259	0.80[CEU][hapmap]
rs4683587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs4683589	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55694384	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55923220	0.81[ASN][1000 genomes]
rs56163421	0.84[ASN][1000 genomes]
rs56254804	0.84[ASN][1000 genomes]
rs57562453	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6439989	0.89[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs6762331	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs6769909	0.81[CEU][hapmap]
rs6794495	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs72982520	0.94[EUR][1000 genomes]
rs72994962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72994967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73869537	0.84[ASN][1000 genomes]
rs73869553	0.86[ASN][1000 genomes]
rs7618821	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs7629005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9682606	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv877551	chr3:140970556-141029860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11713226	ACPL2	cis	parietal	SCAN
rs11713226	RBP2	cis	parietal	SCAN
rs11713226	TRPC1	cis	parietal	SCAN
rs11713226	ACPL2	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:140957800-140973600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:140960000-140980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:140961000-140978800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:140961200-140973600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:140961200-140985800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:140961200-141012600	Weak transcription	Aorta	Aorta
12	chr3:140961400-140974200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:140961400-140974200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:140961400-140974400	Weak transcription	Placenta	Placenta
15	chr3:140961400-140983200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:140961600-140971400	Weak transcription	Fetal Brain Female	brain
17	chr3:140962000-140985800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:140962200-140974200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:140962400-140977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:140962400-140979200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:140962600-140971600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:140962600-140974200	Weak transcription	Spleen	Spleen
23	chr3:140962600-140974600	Weak transcription	Right Atrium	heart
24	chr3:140962600-140975000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:140962600-140978800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:140962600-140979600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:140962600-140980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:140962800-140971000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:140962800-140971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:140963400-140982800	Weak transcription	Brain Germinal Matrix	brain
31	chr3:140963600-140978800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:140964800-140978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:140965400-140971600	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:140966000-140990200	Weak transcription	Psoas Muscle	Psoas
35	chr3:140966200-140974200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:140966200-140979600	Weak transcription	Pancreas	Pancrea
37	chr3:140967000-140971000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:140968000-140976600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:140968200-140979000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:140968200-140990000	Weak transcription	Gastric	stomach
41	chr3:140968400-140982800	Weak transcription	Fetal Lung	lung
42	chr3:140968600-140971600	Weak transcription	Fetal Brain Male	brain
43	chr3:140968800-140974400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:140969200-140972200	Strong transcription	Fetal Stomach	stomach
45	chr3:140969200-140972600	Genic enhancers	Dnd41	blood
46	chr3:140969400-140970600	Enhancers	HSMMtube	muscle
47	chr3:140969600-140974400	Weak transcription	Left Ventricle	heart
48	chr3:140969600-140974600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:140969800-140970600	Enhancers	Fetal Heart	heart
50	chr3:140969800-140971600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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