Variant report

Variant	rs12290996
Chromosome Location	chr11:9987559-9987560
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10500715	0.97[ASN][1000 genomes]
rs10743123	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10770077	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10770078	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840330	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840333	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840334	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840337	0.88[EUR][1000 genomes]
rs10840338	0.90[EUR][1000 genomes]
rs10840359	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042558	0.89[ASN][1000 genomes]
rs11042559	0.85[EUR][1000 genomes]
rs11042561	0.86[EUR][1000 genomes]
rs11042571	0.90[EUR][1000 genomes]
rs11042573	0.85[EUR][1000 genomes]
rs11042574	0.91[ASN][1000 genomes]
rs11042578	0.88[EUR][1000 genomes]
rs11042579	0.87[EUR][1000 genomes]
rs11042580	0.87[EUR][1000 genomes]
rs11602465	0.85[EUR][1000 genomes]
rs11603440	0.87[EUR][1000 genomes]
rs12222953	0.95[ASN][1000 genomes]
rs12419923	0.90[EUR][1000 genomes]
rs12420950	0.84[EUR][1000 genomes]
rs12421200	0.91[EUR][1000 genomes]
rs17271847	0.90[EUR][1000 genomes]
rs17356792	0.90[EUR][1000 genomes]
rs2403226	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403227	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403229	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478985	0.80[EUR][1000 genomes]
rs4529876	0.81[EUR][1000 genomes]
rs4576815	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4909917	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910086	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58084362	0.91[ASN][1000 genomes]
rs60362241	0.91[ASN][1000 genomes]
rs7106914	0.97[ASN][1000 genomes]
rs7114044	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7114303	0.80[EUR][1000 genomes]
rs7131445	0.90[EUR][1000 genomes]
rs7933475	0.99[ASN][1000 genomes]
rs7946995	0.81[EUR][1000 genomes]
rs7951950	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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
3	chr11:9974200-9994400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:9974200-9994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:9974200-9994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
7	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
8	chr11:9977000-9994400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:9979400-9995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:9979600-9994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:9979800-9999200	Weak transcription	NH-A	brain
12	chr11:9981000-10020000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:9981200-9988400	Weak transcription	HMEC	breast
14	chr11:9981200-9990000	Weak transcription	A549	lung
15	chr11:9981200-9990600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:9981200-9995000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:9981200-10004200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:9981200-10009200	Weak transcription	Brain Germinal Matrix	brain
19	chr11:9981400-9989000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:9981400-9989000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:9981400-9989600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr11:9981400-9990600	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:9981400-9990600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:9981400-9992200	Weak transcription	Brain Substantia Nigra	brain
25	chr11:9981400-9993400	Weak transcription	Spleen	Spleen
26	chr11:9981400-9994400	Weak transcription	HUVEC	blood vessel
27	chr11:9981400-9994600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:9981400-9994600	Weak transcription	NHLF	lung
29	chr11:9981400-9994800	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:9981400-9995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:9981400-9995200	Weak transcription	Brain Angular Gyrus	brain
32	chr11:9981400-9995400	Weak transcription	Right Ventricle	heart
33	chr11:9981400-9999000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:9981400-10002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:9981400-10003400	Weak transcription	Brain Anterior Caudate	brain
36	chr11:9981400-10003400	Weak transcription	NHEK	skin
37	chr11:9981400-10003600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:9981400-10004200	Weak transcription	Esophagus	oesophagus
39	chr11:9981400-10004200	Weak transcription	Lung	lung
40	chr11:9981400-10004400	Weak transcription	HepG2	liver
41	chr11:9981400-10008800	Weak transcription	Primary T cells from cord blood	blood
42	chr11:9981400-10010200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:9981400-10014800	Weak transcription	Dnd41	blood
44	chr11:9981400-10017000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
46	chr11:9981600-10003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:9981800-9993600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:9981800-9995200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:9981800-10003400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:9981800-10004800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links