Variant report

Variant	rs10454133
Chromosome Location	chr2:48647871-48647872
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48336922..48340984-chr2:48645140..48651052,10	MCF-7	breast:
2	chr2:48647192..48649423-chr2:48652404..48655156,2	MCF-7	breast:
3	chr2:48337553..48343006-chr2:48644200..48649231,9	MCF-7	breast:
4	chr2:48357074..48359129-chr2:48646502..48648468,2	MCF-7	breast:
5	chr2:48337541..48339290-chr2:48647557..48648526,13	MCF-7	breast:
6	chr2:48337985..48339413-chr2:48647520..48648569,36	MCF-7	breast:
7	chr2:48636349..48637908-chr2:48646875..48649366,2	MCF-7	breast:
8	chr2:48541072..48542749-chr2:48647809..48650233,2	K562	blood:
9	chr2:48342001..48342697-chr2:48647600..48648543,2	K562	blood:
10	chr2:48540164..48542701-chr2:48646519..48648183,2	MCF-7	breast:
11	chr2:48647311..48649443-chr2:48666220..48667845,2	MCF-7	breast:
12	chr2:48338306..48339005-chr2:48647700..48648301,2	MCF-7	breast:
13	chr2:48337971..48339938-chr2:48647597..48648547,19	K562	blood:
14	chr2:48540490..48542978-chr2:48647661..48649462,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10186237	0.89[CEU][hapmap]
rs10199431	0.82[CEU][hapmap]
rs10208627	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10211336	0.94[ASN][1000 genomes]
rs10454134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10495951	0.83[JPT][hapmap]
rs10495952	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs11676168	0.89[CEU][hapmap];0.95[MEX][hapmap]
rs11679523	0.83[JPT][hapmap]
rs11680719	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11680916	0.82[JPT][hapmap]
rs11682044	0.95[MEX][hapmap]
rs11682931	0.83[AMR][1000 genomes]
rs11683639	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11683708	0.94[ASN][1000 genomes]
rs11685861	0.89[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11688481	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs11689622	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11690690	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs11690748	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs11690845	0.83[JPT][hapmap]
rs12105983	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13388291	0.82[CEU][hapmap]
rs13392004	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13399936	0.97[ASN][1000 genomes]
rs13400909	0.97[ASN][1000 genomes]
rs13401749	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs13401752	0.97[ASN][1000 genomes]
rs13429377	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13432998	0.85[MEX][hapmap]
rs17037289	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs17037298	0.83[JPT][hapmap]
rs17855177	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4267555	0.88[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4274640	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316980	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4344965	0.81[CEU][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs4411759	0.89[CEU][hapmap];0.95[MEX][hapmap]
rs4438532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4494796	0.98[ASN][1000 genomes]
rs4497915	0.84[TSI][hapmap]
rs4606978	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4638844	0.90[ASN][1000 genomes]
rs55640438	0.98[ASN][1000 genomes]
rs55757090	0.91[ASN][1000 genomes]
rs55971719	0.91[ASN][1000 genomes]
rs56365822	0.86[ASN][1000 genomes]
rs58020097	0.97[ASN][1000 genomes]
rs58969359	0.97[ASN][1000 genomes]
rs58978223	0.85[ASN][1000 genomes]
rs59045263	0.82[ASN][1000 genomes]
rs60042255	0.86[ASN][1000 genomes]
rs60988618	0.95[ASN][1000 genomes]
rs61303367	0.85[ASN][1000 genomes]
rs62137015	0.83[AMR][1000 genomes]
rs62137018	0.89[ASN][1000 genomes]
rs62137019	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137021	0.84[ASN][1000 genomes]
rs62137041	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545027	0.84[CEU][hapmap]
rs6545030	0.85[CEU][hapmap]
rs6545036	0.92[CEU][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6545039	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66705539	0.84[ASN][1000 genomes]
rs6705802	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs6712029	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs6718068	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs6732196	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735288	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6743757	0.88[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs6747441	0.85[ASN][1000 genomes]
rs6749773	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820454	0.86[ASN][1000 genomes]
rs72820474	1.00[ASN][1000 genomes]
rs72820479	0.99[ASN][1000 genomes]
rs72820484	0.97[ASN][1000 genomes]
rs72820492	0.95[ASN][1000 genomes]
rs72820494	0.97[ASN][1000 genomes]
rs72820499	0.96[ASN][1000 genomes]
rs7562069	0.81[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs7562816	0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs7565792	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7566239	0.83[JPT][hapmap]
rs7568574	0.82[ASN][1000 genomes]
rs7576964	0.81[CHD][hapmap];0.82[MEX][hapmap]
rs7577237	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs7579932	0.89[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7600794	0.89[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs7606104	0.89[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10454133	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48643600-48651200	Weak transcription	Psoas Muscle	Psoas
2	chr2:48645200-48651000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:48645800-48648600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:48646600-48648400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:48646600-48648400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:48646800-48648000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:48646800-48648200	Enhancers	Spleen	Spleen
8	chr2:48646800-48648400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:48646800-48648400	Enhancers	HMEC	breast
10	chr2:48647000-48648000	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr2:48647000-48648000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:48647000-48648000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr2:48647000-48648000	Enhancers	Right Atrium	heart
14	chr2:48647000-48648200	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:48647000-48648200	Enhancers	Placenta	Placenta
16	chr2:48647000-48648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:48647000-48648400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:48647200-48648000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:48647200-48648000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr2:48647200-48648000	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr2:48647200-48648000	Enhancers	Right Ventricle	heart
22	chr2:48647200-48648000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:48647200-48648200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr2:48647200-48648200	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr2:48647200-48648400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:48647200-48648400	Enhancers	Primary B cells from cord blood	blood
27	chr2:48647200-48648400	Enhancers	Primary T cells from cord blood	blood
28	chr2:48647200-48648400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr2:48647200-48648400	Enhancers	NHEK	skin
30	chr2:48647400-48648000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:48647400-48648000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr2:48647400-48648000	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr2:48647400-48648000	Enhancers	Colonic Mucosa	Colon
34	chr2:48647400-48648000	Enhancers	Fetal Brain Male	brain
35	chr2:48647400-48648000	Enhancers	NH-A	brain
36	chr2:48647400-48648200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:48647400-48648200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:48647400-48648400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr2:48647400-48648400	Flanking Active TSS	Liver	Liver
40	chr2:48647400-48648400	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:48647600-48648000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr2:48647600-48648000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:48647600-48648000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:48647600-48648000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr2:48647600-48648000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr2:48647600-48648000	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:48647600-48648000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:48647600-48648000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:48647600-48648000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr2:48647600-48648000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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