Variant report

Variant	rs10899225
Chromosome Location	chr11:76192332-76192333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:76191502..76194293-chr11:76198687..76201522,2	MCF-7	breast:
2	chr11:76190688..76192947-chr11:76198433..76201383,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10793167	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793169	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793171	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10899217	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10899219	0.87[AFR][1000 genomes]
rs10899220	0.88[AFR][1000 genomes]
rs10899222	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10899227	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236749	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236752	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11606394	0.89[AFR][1000 genomes]
rs2508738	0.84[AFR][1000 genomes]
rs2508740	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2508741	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2508753	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508756	0.80[AFR][1000 genomes]
rs2508759	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2508760	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508761	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2508762	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2513505	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2513508	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2513513	0.80[AMR][1000 genomes]
rs2513515	0.88[AFR][1000 genomes]
rs2513520	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2513523	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3016373	0.87[AFR][1000 genomes]
rs3814711	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4245443	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4272809	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300410	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625500	0.87[AFR][1000 genomes]
rs4945087	0.84[AFR][1000 genomes]
rs4945090	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5023625	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592635	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7106564	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7107058	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109548	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7926009	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940390	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3383733	chr11:76186353-76225544	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76166800-76219400	Weak transcription	Small Intestine	intestine
2	chr11:76168800-76234800	Weak transcription	Psoas Muscle	Psoas
3	chr11:76171200-76221200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:76177400-76195400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:76180200-76204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:76182800-76192400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:76183800-76194400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:76184400-76235000	Weak transcription	NHEK	skin
9	chr11:76184800-76202600	Weak transcription	Aorta	Aorta
10	chr11:76185000-76204000	Weak transcription	Right Ventricle	heart
11	chr11:76185400-76193400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:76187000-76192400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:76188400-76193000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:76189000-76192400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:76189000-76192800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:76189000-76231400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr11:76189200-76211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:76189400-76223000	Weak transcription	HUVEC	blood vessel
19	chr11:76189600-76193200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:76190000-76192400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:76190000-76192600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr11:76190000-76192800	Strong transcription	Fetal Lung	lung
23	chr11:76190000-76193800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:76190200-76192400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:76190200-76192400	Strong transcription	Fetal Muscle Leg	muscle
26	chr11:76190200-76192400	Strong transcription	Thymus	Thymus
27	chr11:76190200-76192600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:76190200-76192600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:76190200-76192600	Strong transcription	Adipose Nuclei	Adipose
30	chr11:76190200-76192600	Strong transcription	Liver	Liver
31	chr11:76190200-76192600	Strong transcription	Brain Anterior Caudate	brain
32	chr11:76190200-76192600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr11:76190200-76192600	Strong transcription	Ovary	ovary
34	chr11:76190200-76192800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr11:76190200-76192800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:76190200-76192800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:76190200-76192800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:76190200-76192800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:76190200-76193000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:76190200-76193000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr11:76190200-76193000	Strong transcription	Spleen	Spleen
42	chr11:76190200-76193200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:76190200-76193600	Strong transcription	Placenta	Placenta
44	chr11:76190200-76193800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:76190200-76193800	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr11:76190400-76192400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:76190600-76193800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:76190600-76207200	Weak transcription	Brain Substantia Nigra	brain
49	chr11:76190800-76234200	Weak transcription	Left Ventricle	heart
50	chr11:76191000-76192800	ZNF genes & repeats	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links