Variant report

Variant	rs12421053
Chromosome Location	chr11:73276900-73276901
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	chr11:73265451..73268306-chr11:73275988..73278927,2	K562	blood:
2	chr11:73275181..73277869-chr11:73279088..73282119,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1002126	0.81[CEU][hapmap]
rs10047442	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs10793060	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs10898920	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10898925	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235743	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11235746	0.93[CEU][hapmap]
rs11820786	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11823979	0.86[EUR][1000 genomes]
rs11826896	0.80[GIH][hapmap]
rs12276536	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12295744	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939382	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs2366780	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741148	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs4944845	0.90[ASN][1000 genomes]
rs55751428	0.93[ASN][1000 genomes]
rs6592523	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs7114009	0.82[YRI][hapmap]
rs7119167	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127171	0.95[ASN][1000 genomes]
rs73542998	0.95[ASN][1000 genomes]
rs7925573	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs7935204	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945596	0.90[ASN][1000 genomes]
rs7948630	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950002	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952686	0.94[CEU][hapmap]
rs876480	1.00[CHB][hapmap]
rs880317	0.94[CEU][hapmap];0.85[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs947837	1.00[CHB][hapmap]

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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv983188	chr11:73273934-73307064	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12421053	ARHGEF17	cis	multi-tissue	Pritchard
rs12421053	ANO1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73243400-73279600	Weak transcription	Fetal Stomach	stomach
2	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:73250200-73278800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:73250800-73282800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:73251000-73288800	Weak transcription	Thymus	Thymus
6	chr11:73253800-73307000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:73258800-73278000	Weak transcription	Primary B cells from cord blood	blood
8	chr11:73262200-73281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:73263200-73306000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:73263800-73288800	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:73264600-73287000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:73265400-73287200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:73266400-73280000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:73266600-73307800	Weak transcription	Fetal Intestine Small	intestine
15	chr11:73267200-73277000	Weak transcription	Primary T cells from cord blood	blood
16	chr11:73267400-73281400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:73267400-73284800	Weak transcription	Right Atrium	heart
18	chr11:73268400-73281000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:73269800-73279600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:73270600-73288000	Weak transcription	NHLF	lung
21	chr11:73271400-73277400	Weak transcription	Left Ventricle	heart
22	chr11:73271400-73277600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:73272000-73277800	Weak transcription	Esophagus	oesophagus
24	chr11:73272200-73307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:73274600-73287000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:73274600-73287000	Weak transcription	Brain Substantia Nigra	brain
27	chr11:73274800-73290800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr11:73275000-73277200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr11:73275200-73286800	Weak transcription	Brain Anterior Caudate	brain
30	chr11:73275200-73287000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:73275400-73277200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:73275400-73278000	Weak transcription	Fetal Thymus	thymus
33	chr11:73275400-73284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:73275400-73288800	Weak transcription	GM12878-XiMat	blood
35	chr11:73275400-73307000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:73275600-73277800	Weak transcription	Right Ventricle	heart
37	chr11:73275600-73278000	Weak transcription	Psoas Muscle	Psoas
38	chr11:73276000-73277600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:73276200-73277000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:73276200-73277000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr11:73276200-73278600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr11:73276200-73287200	Weak transcription	Brain Angular Gyrus	brain
43	chr11:73276400-73277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:73276400-73277400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr11:73276400-73277600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr11:73276400-73277800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:73276400-73278000	Weak transcription	K562	blood
48	chr11:73276400-73278600	Weak transcription	Dnd41	blood
49	chr11:73276400-73287400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:73276400-73289800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links