Variant report

Variant	rs11238520
Chromosome Location	chr10:43857793-43857794
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43856272..43860710-chr10:43899954..43905301,8	MCF-7	breast:
2	chr10:43787258..43789990-chr10:43857247..43859004,2	MCF-7	breast:
3	chr10:43845683..43851518-chr10:43853877..43859694,14	MCF-7	breast:
4	chr10:43851891..43853491-chr10:43856042..43858143,2	MCF-7	breast:
5	chr10:43855555..43859405-chr10:43889416..43893889,5	MCF-7	breast:
6	chr10:43856738..43859164-chr10:43866912..43868599,2	MCF-7	breast:
7	chr10:43856477..43861777-chr10:43890250..43893117,4	MCF-7	breast:
8	chr10:43856796..43859444-chr10:43950333..43952475,2	MCF-7	breast:
9	chr10:43811335..43814194-chr10:43855788..43859216,3	MCF-7	breast:
10	chr10:43857548..43859607-chr10:43913641..43916534,2	MCF-7	breast:
11	chr10:43843670..43847999-chr10:43855800..43861023,11	MCF-7	breast:
12	chr10:43571829..43574685-chr10:43855832..43858827,2	MCF-7	breast:
13	chr10:43855373..43860700-chr10:43866814..43875446,19	MCF-7	breast:
14	chr10:43855397..43862555-chr10:43901834..43907536,13	MCF-7	breast:
15	chr10:43857152..43860399-chr10:43897567..43900656,3	MCF-7	breast:
16	chr10:43856971..43858814-chr10:43891755..43893439,2	K562	blood:
17	chr10:43857446..43858092-chr14:31676755..31677684,2	HCT-116	colon:
18	chr10:43853521..43859723-chr10:43870896..43875408,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169813	Chromatin interaction
ENSG00000092148	Chromatin interaction
ENSG00000165731	Chromatin interaction
ENSG00000230555	Chromatin interaction
ENSG00000150201	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11238518	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238519	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238531	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238533	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238547	1.00[ASN][1000 genomes]
rs11238570	1.00[ASN][1000 genomes]
rs12356024	1.00[ASN][1000 genomes]
rs12356570	1.00[ASN][1000 genomes]
rs12359520	1.00[ASN][1000 genomes]
rs12359825	1.00[ASN][1000 genomes]
rs12359980	1.00[ASN][1000 genomes]
rs17366560	1.00[ASN][1000 genomes]
rs4646975	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948720	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56120769	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60163354	1.00[ASN][1000 genomes]
rs61845676	1.00[ASN][1000 genomes]
rs61845680	1.00[ASN][1000 genomes]
rs61845682	1.00[ASN][1000 genomes]
rs61858993	1.00[ASN][1000 genomes]
rs61858995	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61859001	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61859441	1.00[ASN][1000 genomes]
rs61859445	1.00[ASN][1000 genomes]
rs61859998	1.00[ASN][1000 genomes]
rs61860007	1.00[ASN][1000 genomes]
rs61860889	1.00[ASN][1000 genomes]
rs67284218	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7073767	1.00[ASN][1000 genomes]
rs7079012	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084706	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093434	1.00[ASN][1000 genomes]
rs7100846	1.00[ASN][1000 genomes]
rs7900284	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7905073	1.00[ASN][1000 genomes]
rs7920408	0.82[AMR][1000 genomes];1.00[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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 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	chr10:43856600-43858600	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:43857000-43858000	Active TSS	Colonic Mucosa	Colon
3	chr10:43857000-43858000	Active TSS	Duodenum Mucosa	Duodenum
4	chr10:43857000-43858200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr10:43857000-43858200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr10:43857000-43858200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr10:43857000-43858200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr10:43857000-43858200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr10:43857000-43858200	Active TSS	Fetal Intestine Large	intestine
10	chr10:43857000-43858400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr10:43857000-43858400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr10:43857000-43858400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr10:43857000-43858400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr10:43857000-43858400	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr10:43857000-43858400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr10:43857000-43858400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:43857000-43858400	Active TSS	Brain Angular Gyrus	brain
18	chr10:43857000-43858600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr10:43857000-43858600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:43857000-43858600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:43857200-43857800	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr10:43857200-43857800	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr10:43857200-43857800	Flanking Active TSS	Fetal Brain Male	brain
24	chr10:43857200-43858000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr10:43857200-43858000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:43857200-43858000	Active TSS	Brain Anterior Caudate	brain
27	chr10:43857200-43858000	Active TSS	Placenta Amnion	Placenta Amnion
28	chr10:43857200-43858200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:43857200-43858200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr10:43857200-43858200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr10:43857200-43858200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr10:43857200-43858200	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr10:43857200-43858200	Active TSS	Fetal Lung	lung
34	chr10:43857200-43858200	Active TSS	Small Intestine	intestine
35	chr10:43857200-43858200	Active TSS	NH-A	brain
36	chr10:43857200-43858400	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr10:43857200-43858400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:43857200-43858400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:43857200-43858400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:43857200-43858400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr10:43857200-43858400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr10:43857200-43858400	Flanking Active TSS	Liver	Liver
43	chr10:43857200-43858400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr10:43857200-43858400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr10:43857200-43858400	Active TSS	Fetal Kidney	kidney
46	chr10:43857200-43858400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr10:43857200-43858400	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr10:43857200-43858400	Flanking Active TSS	Placenta	Placenta
49	chr10:43857200-43858400	Flanking Active TSS	Left Ventricle	heart
50	chr10:43857200-43858400	Flanking Active TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links