Variant report

Variant	rs12223991
Chromosome Location	chr11:102105723-102105724
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:102105617-102106194	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:102105589-102105726	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:102105376-102106591	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:102105684-102106102	HCT-116	colon:	n/a	n/a
5	POLR2A	chr11:102105350-102107540	Hela-S3	cervix:	n/a	n/a
6	FOSL2	chr11:102105691-102106095	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102105024..102105732-chr3:111632640..111633407,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254422	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10895272	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895273	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895274	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895275	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10895276	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10895277	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895278	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895280	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10895282	0.80[ASN][1000 genomes]
rs11225156	0.86[EUR][1000 genomes]
rs11225160	0.86[EUR][1000 genomes]
rs11225163	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11225165	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11225167	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11225170	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11225174	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225177	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605954	0.83[EUR][1000 genomes]
rs11608234	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12226331	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12420287	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12421242	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12786272	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12787996	0.88[EUR][1000 genomes]
rs12790399	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12793501	0.81[EUR][1000 genomes]
rs12795624	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12807220	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17097547	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17097560	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1820455	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1893498	0.84[EUR][1000 genomes]
rs2187525	0.82[EUR][1000 genomes]
rs2282652	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3858420	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4447144	0.82[EUR][1000 genomes]
rs4475891	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4754041	0.82[EUR][1000 genomes]
rs57027482	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58751289	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61280272	0.87[ASN][1000 genomes]
rs7110557	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7112802	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120067	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7122907	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124247	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs718891	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7931576	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7942061	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8504	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102079000-102107200	Weak transcription	Fetal Brain Male	brain
2	chr11:102081200-102118600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:102086800-102111600	Weak transcription	Lung	lung
4	chr11:102093000-102113000	Weak transcription	Ovary	ovary
5	chr11:102095200-102118600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:102096800-102114600	Weak transcription	Small Intestine	intestine
7	chr11:102097000-102105800	Weak transcription	Right Ventricle	heart
8	chr11:102097200-102105800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr11:102097800-102119600	Weak transcription	Right Atrium	heart
10	chr11:102098000-102111600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:102098400-102105800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:102098400-102106600	Strong transcription	HSMM	muscle
13	chr11:102098400-102118600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:102098600-102105800	Weak transcription	Psoas Muscle	Psoas
15	chr11:102099000-102112800	Weak transcription	Hela-S3	cervix
16	chr11:102100800-102109000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:102100800-102111400	Weak transcription	A549	lung
18	chr11:102100800-102112800	Weak transcription	Fetal Heart	heart
19	chr11:102100800-102113000	Weak transcription	Esophagus	oesophagus
20	chr11:102101000-102107800	Weak transcription	Fetal Kidney	kidney
21	chr11:102101000-102111200	Weak transcription	NHLF	lung
22	chr11:102101200-102105800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:102101200-102107800	Weak transcription	HSMMtube	muscle
24	chr11:102101200-102108800	Weak transcription	Fetal Intestine Large	intestine
25	chr11:102101600-102107400	Weak transcription	Placenta	Placenta
26	chr11:102101600-102107600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:102101800-102106000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:102101800-102112800	Weak transcription	Liver	Liver
29	chr11:102102000-102105800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:102102000-102107400	Weak transcription	Adipose Nuclei	Adipose
31	chr11:102102000-102115400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:102102200-102107400	Weak transcription	HepG2	liver
33	chr11:102102200-102111600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:102103800-102107400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:102104600-102106000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:102104600-102118600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:102104800-102106200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:102104800-102106800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:102105000-102106000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:102105000-102107200	Weak transcription	HMEC	breast
41	chr11:102105000-102118600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:102105200-102105800	Enhancers	NHDF-Ad	bronchial
43	chr11:102105200-102106000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:102105200-102106200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr11:102105200-102107200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:102105200-102107400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:102105200-102107600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:102105200-102109000	Weak transcription	Fetal Intestine Small	intestine
49	chr11:102105200-102118600	Weak transcription	Fetal Muscle Leg	muscle
50	chr11:102105200-102118600	Weak transcription	Fetal Stomach	stomach

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