Variant report

Variant	rs12420463
Chromosome Location	chr11:9264368-9264369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9261606..9264220-chr11:9264222..9265740,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM41B-1	chr11:9263995-9264376	ENSG00000255097.1

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10770000	0.90[ASN][1000 genomes]
rs10770001	0.90[ASN][1000 genomes]
rs11042227	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042245	0.85[ASN][1000 genomes]
rs11602591	0.87[AMR][1000 genomes]
rs11608172	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12289113	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12295767	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12296016	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12577661	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12796666	0.85[AMR][1000 genomes]
rs12801814	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2133216	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2873069	0.90[ASN][1000 genomes]
rs34446443	0.85[AMR][1000 genomes]
rs34494849	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34716494	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34729888	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35381016	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35757766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35955530	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61875672	0.87[AMR][1000 genomes]
rs61875673	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61877814	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6486210	0.88[ASN][1000 genomes]
rs6486215	0.86[ASN][1000 genomes]
rs6486226	0.93[ASN][1000 genomes]
rs6486231	0.90[ASN][1000 genomes]
rs7104221	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7109911	0.85[ASN][1000 genomes]
rs7112540	0.86[ASN][1000 genomes]
rs7114688	0.90[ASN][1000 genomes]
rs7115062	0.93[ASN][1000 genomes]
rs7116459	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7124178	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7396439	0.86[ASN][1000 genomes]
rs7482630	0.89[ASN][1000 genomes]
rs770	0.90[ASN][1000 genomes]
rs7924664	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7933448	0.91[ASN][1000 genomes]
rs7941520	0.90[ASN][1000 genomes]
rs7951700	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs952374	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9736263	0.88[ASN][1000 genomes]
rs9888193	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9888229	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9251000-9271600	Weak transcription	Hela-S3	cervix
2	chr11:9251000-9274400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr11:9251400-9271800	Weak transcription	Gastric	stomach
4	chr11:9252600-9272400	Weak transcription	Spleen	Spleen
5	chr11:9252600-9272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:9253000-9265000	Weak transcription	K562	blood
7	chr11:9253000-9285600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:9253200-9269600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:9253200-9274600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:9253600-9268200	Weak transcription	HepG2	liver
11	chr11:9253800-9271400	Weak transcription	HSMM	muscle
12	chr11:9254200-9267600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:9254400-9267600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:9254400-9271600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:9254400-9271800	Weak transcription	Osteobl	bone
16	chr11:9254400-9272400	Weak transcription	Ovary	ovary
17	chr11:9254400-9274600	Weak transcription	Colon Smooth Muscle	Colon
18	chr11:9254400-9280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:9254600-9267600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr11:9255200-9271800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:9255400-9269600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:9256600-9274400	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:9257000-9276000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:9257000-9284800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:9257200-9285600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:9257600-9276800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:9258400-9267400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:9258400-9267600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:9259000-9267600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:9259200-9271600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:9259400-9266200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:9260800-9267600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr11:9261800-9265200	Enhancers	Brain Substantia Nigra	brain
34	chr11:9261800-9285600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:9262000-9267400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:9262200-9264400	Enhancers	GM12878-XiMat	blood
37	chr11:9262200-9265200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr11:9262200-9271400	Weak transcription	Left Ventricle	heart
39	chr11:9262200-9274600	Weak transcription	Fetal Stomach	stomach
40	chr11:9262400-9264400	Enhancers	Brain Angular Gyrus	brain
41	chr11:9262400-9267400	Weak transcription	Fetal Thymus	thymus
42	chr11:9262400-9267800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr11:9262400-9282400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:9262600-9267400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr11:9262800-9267200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:9262800-9271600	Weak transcription	Fetal Heart	heart
47	chr11:9262800-9271800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:9263000-9274600	Weak transcription	Psoas Muscle	Psoas
49	chr11:9263200-9269400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:9263600-9264400	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links