Variant report

Variant	rs1544862
Chromosome Location	chr11:10679759-10679760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10675148..10677906-chr11:10678421..10681418,4	MCF-7	breast:
2	chr11:10678901..10680801-chr11:10754781..10757131,2	MCF-7	breast:
3	chr11:10678917..10680760-chr11:10757378..10759987,2	K562	blood:
4	chr11:10679153..10681988-chr11:10698825..10701306,2	K562	blood:
5	chr11:10679397..10680975-chr11:10707592..10709737,2	K562	blood:
6	chr11:10679384..10682080-chr20:56827072..56828747,2	MCF-7	breast:
7	chr11:10674925..10678334-chr11:10679453..10682484,4	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10219376	0.82[EUR][1000 genomes]
rs10431031	0.86[EUR][1000 genomes]
rs10770128	0.87[ASW][hapmap];0.95[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs10770129	0.90[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10770130	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770132	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10770133	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10840451	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs10840454	0.93[EUR][1000 genomes]
rs10840455	0.95[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs10840456	0.90[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840458	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10840459	0.89[ASN][1000 genomes]
rs10840460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840461	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840464	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840465	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840466	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840467	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840468	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11042909	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11042910	0.85[JPT][hapmap]
rs11042911	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11042913	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12363422	0.85[ASN][1000 genomes]
rs12420672	0.85[ASN][1000 genomes]
rs12420675	0.85[ASN][1000 genomes]
rs1390572	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390573	0.87[ASN][1000 genomes]
rs1425149	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544863	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs16908157	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs16908159	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs16908162	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1845832	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874444	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098840	0.95[ASN][1000 genomes]
rs34554801	0.89[ASN][1000 genomes]
rs35040034	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35165550	0.85[ASN][1000 genomes]
rs4243916	0.87[ASN][1000 genomes]
rs4909946	0.87[ASN][1000 genomes]
rs4910166	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7123106	0.81[EUR][1000 genomes]
rs7127014	0.83[EUR][1000 genomes]
rs722274	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745336	0.87[ASN][1000 genomes]
rs750540	0.85[ASN][1000 genomes]
rs7925193	0.90[JPT][hapmap]
rs7933525	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935285	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs7938027	0.87[ASN][1000 genomes]
rs7938635	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7939662	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7939686	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs881870	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs903825	0.85[ASN][1000 genomes]
rs903826	0.85[ASN][1000 genomes]
rs903827	0.85[ASN][1000 genomes]
rs903828	0.85[ASN][1000 genomes]
rs9633862	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9633863	0.88[EUR][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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3327021	chr11:10679466-10679950	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1544862	RRAS2	cis	cerebellum	SCAN
rs1544862	PLA2G7	trans	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10673000-10682200	Enhancers	Placenta	Placenta
2	chr11:10673400-10682800	Enhancers	Ovary	ovary
3	chr11:10673800-10681400	Weak transcription	Pancreas	Pancrea
4	chr11:10674000-10681400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:10674200-10681800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr11:10674400-10681400	Enhancers	Fetal Muscle Leg	muscle
7	chr11:10674400-10681800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr11:10674600-10689600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:10675800-10680000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:10676000-10683200	Enhancers	NHDF-Ad	bronchial
11	chr11:10676400-10683400	Genic enhancers	Fetal Stomach	stomach
12	chr11:10676600-10681600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:10676800-10679800	Enhancers	Fetal Intestine Large	intestine
14	chr11:10677000-10681800	Enhancers	HSMMtube	muscle
15	chr11:10677000-10682200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:10677000-10683400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:10677200-10682800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:10677400-10679800	Enhancers	Fetal Muscle Trunk	muscle
19	chr11:10677400-10680600	Genic enhancers	NHLF	lung
20	chr11:10677400-10680800	Enhancers	Small Intestine	intestine
21	chr11:10677400-10682200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr11:10677400-10683000	Enhancers	Spleen	Spleen
23	chr11:10677600-10680600	Weak transcription	Primary B cells from cord blood	blood
24	chr11:10678000-10680200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:10678000-10680600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:10678200-10681000	Enhancers	Colonic Mucosa	Colon
27	chr11:10678200-10681400	Enhancers	Lung	lung
28	chr11:10678200-10681600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr11:10678200-10682000	Enhancers	Adipose Nuclei	Adipose
30	chr11:10678400-10679800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:10678400-10681400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr11:10678400-10682200	Enhancers	Brain Anterior Caudate	brain
33	chr11:10678400-10682200	Enhancers	Esophagus	oesophagus
34	chr11:10678400-10682200	Enhancers	Right Atrium	heart
35	chr11:10678400-10682400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:10678400-10682600	Enhancers	Left Ventricle	heart
37	chr11:10678600-10680000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr11:10678600-10680000	Flanking Active TSS	GM12878-XiMat	blood
39	chr11:10678600-10681600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:10678600-10681800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr11:10678600-10682000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:10678600-10682200	Enhancers	Right Ventricle	heart
43	chr11:10678800-10679800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:10678800-10680000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr11:10678800-10680000	Enhancers	Primary B cells from peripheral blood	blood
46	chr11:10678800-10680000	Enhancers	Primary hematopoietic stem cells	blood
47	chr11:10678800-10680000	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr11:10678800-10680200	Flanking Active TSS	K562	blood
49	chr11:10678800-10680600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:10678800-10680600	Enhancers	A549	lung

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