Variant report

Variant	rs11188234
Chromosome Location	chr10:96988739-96988740
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96983667..96985290-chr10:96987249..96989514,2	MCF-7	breast:
2	chr10:96988601..96990244-chr10:96996425..96998002,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1049814	0.94[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1049921	0.91[EUR][1000 genomes]
rs10882573	0.93[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11188231	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188247	0.94[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12355731	0.81[AFR][1000 genomes]
rs12357280	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17452807	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs45550034	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61887990	0.81[AFR][1000 genomes]
rs7894326	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1834151	chr10:96925446-96992955	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11188234	FRAT2	cis	parietal	SCAN
rs11188234	ANKRD42	trans	cerebellum	SCAN
rs11188234	PDLIM1	cis	cerebellum	SCAN
rs11188234	PCGF5	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96944200-96990400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr10:96956200-96990400	Weak transcription	Aorta	Aorta
3	chr10:96960200-96988800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr10:96961800-96989400	Weak transcription	Primary T cells from cord blood	blood
5	chr10:96962000-96990000	Weak transcription	Fetal Intestine Small	intestine
6	chr10:96965400-96989400	Weak transcription	Fetal Intestine Large	intestine
7	chr10:96969200-96990200	Weak transcription	Left Ventricle	heart
8	chr10:96969400-96990400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:96970200-96992400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:96971800-96989400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:96972600-96989600	Weak transcription	Fetal Thymus	thymus
12	chr10:96975400-96990200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:96975600-96990000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr10:96976000-96990000	Weak transcription	Primary B cells from cord blood	blood
15	chr10:96976400-96989600	Weak transcription	GM12878-XiMat	blood
16	chr10:96980200-96989400	Weak transcription	Fetal Heart	heart
17	chr10:96981800-96989200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:96982400-96990200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr10:96984600-96990400	Weak transcription	Esophagus	oesophagus
20	chr10:96985200-96989400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:96986400-96990400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr10:96987000-96990200	Weak transcription	Right Ventricle	heart
23	chr10:96987200-96989200	Enhancers	A549	lung
24	chr10:96987400-96990800	Enhancers	NHDF-Ad	bronchial
25	chr10:96987600-96988800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:96987800-96989000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:96987800-96989200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr10:96987800-96989200	Enhancers	NH-A	brain
29	chr10:96987800-96989200	Enhancers	NHEK	skin
30	chr10:96987800-96989400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr10:96987800-96991000	Enhancers	HMEC	breast
32	chr10:96988000-96989000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr10:96988000-96989200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr10:96988000-96989200	Enhancers	NHLF	lung
35	chr10:96988000-96989200	Enhancers	Osteobl	bone
36	chr10:96988000-96989400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr10:96988000-96989400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr10:96988000-96989800	Enhancers	HSMMtube	muscle
39	chr10:96988000-96990000	Weak transcription	Fetal Kidney	kidney
40	chr10:96988000-96990400	Enhancers	HSMM	muscle
41	chr10:96988000-96990800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:96988200-96989200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:96988200-96989200	Weak transcription	Adipose Nuclei	Adipose
44	chr10:96988200-96989600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr10:96988200-96989800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr10:96988200-96990400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:96988200-96990400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:96988200-96990400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:96988400-96988800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr10:96988400-96989200	Enhancers	HUES64 Cell Line	embryonic stem cell

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