Variant report

Variant	rs3225
Chromosome Location	chr11:120100520-120100521
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120042666..120043739-chr11:120100070..120101150,7	K562	blood:
2	chr11:120100473..120102218-chr11:120106489..120108634,2	MCF-7	breast:
3	chr11:120098962..120101044-chr11:120122301..120123827,2	K562	blood:
4	chr11:120099434..120101938-chr11:120172403..120174898,2	K562	blood:
5	chr11:120041545..120045663-chr11:120098074..120102653,6	MCF-7	breast:
6	chr11:120043046..120043571-chr11:120100218..120100788,2	MCF-7	breast:
7	chr11:120091006..120093784-chr11:120097633..120101741,5	K562	blood:
8	chr11:120040154..120042795-chr11:120100030..120102523,3	K562	blood:
9	chr11:119993941..119995703-chr11:120098281..120100957,2	MCF-7	breast:
10	chr11:120099751..120100618-chr11:120170383..120171309,2	K562	blood:
11	chr11:120042675..120043623-chr11:120099973..120101146,10	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM29-3	chr11:120099738-120101127	NONHSAT024720

No data

Variant related genes	Relation type
ENSG00000137709	Chromatin interaction
ENSG00000137699	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1295019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444242	0.92[CEU][hapmap]
rs2465654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2508489	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2508496	0.92[CEU][hapmap]
rs2845706	0.93[AFR][1000 genomes]
rs2845708	0.85[CEU][hapmap]
rs472948	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs477863	0.92[CEU][hapmap]
rs505142	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs521841	0.92[CEU][hapmap]
rs580174	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs692804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120084200-120102600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:120091000-120102800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:120092800-120102000	Weak transcription	Brain Angular Gyrus	brain
4	chr11:120093600-120100600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:120094800-120100800	Weak transcription	Stomach Mucosa	stomach
6	chr11:120096000-120100600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr11:120096000-120100600	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:120096200-120100600	Weak transcription	Fetal Kidney	kidney
9	chr11:120096400-120101000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr11:120096400-120101200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:120096400-120102200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:120096600-120100600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:120096600-120100800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:120096600-120110800	Weak transcription	Right Atrium	heart
15	chr11:120096800-120101000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:120096800-120102400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:120097000-120101200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:120097000-120103000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:120097200-120101000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:120097200-120106200	Weak transcription	Esophagus	oesophagus
21	chr11:120097400-120102000	Strong transcription	Fetal Intestine Large	intestine
22	chr11:120097600-120101600	Strong transcription	Liver	Liver
23	chr11:120097600-120102800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr11:120097800-120101000	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:120097800-120102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:120098200-120102200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:120098200-120102400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:120098400-120100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:120098400-120101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:120098600-120100600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:120098600-120101600	Weak transcription	Brain Anterior Caudate	brain
32	chr11:120098600-120102600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:120098600-120104400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:120098600-120105400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:120099000-120101400	Weak transcription	Right Ventricle	heart
36	chr11:120099400-120101200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:120099600-120100600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:120099600-120100600	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr11:120099800-120100600	Genic enhancers	Fetal Stomach	stomach
40	chr11:120099800-120100800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:120099800-120102400	Weak transcription	Adipose Nuclei	Adipose
42	chr11:120099800-120110800	Weak transcription	Ovary	ovary
43	chr11:120100000-120101000	Strong transcription	Fetal Lung	lung
44	chr11:120100000-120101400	Weak transcription	Gastric	stomach
45	chr11:120100000-120102400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:120100200-120100600	Genic enhancers	Fetal Intestine Small	intestine
47	chr11:120100200-120102000	Weak transcription	HepG2	liver
48	chr11:120100200-120104200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:120100200-120104200	Weak transcription	Pancreas	Pancrea
50	chr11:120100400-120100600	Enhancers	Stomach Smooth Muscle	stomach

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