Variant report

Variant	rs592577
Chromosome Location	chr18:11993748-11993749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11992964..11995381-chr18:12038056..12040567,2	MCF-7	breast:
2	chr18:11987852..11990240-chr18:11991809..11994085,2	K562	blood:
3	chr18:11979171..11983679-chr18:11993501..11995734,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141401	Chromatin interaction
ENSG00000266995	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs3859296	0.92[ASN][1000 genomes]
rs58393627	0.95[ASN][1000 genomes]
rs588257	0.92[ASN][1000 genomes]
rs589247	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs590100	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs590277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591061	0.90[ASN][1000 genomes]
rs604962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605047	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605964	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606020	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606105	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606478	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs607200	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs622061	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs622246	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs636173	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636300	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs638063	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs638125	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs649396	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs649713	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs650727	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs655790	0.96[ASN][1000 genomes]
rs666521	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs667798	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs668223	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs669838	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682271	0.92[ASN][1000 genomes]
rs683190	0.92[ASN][1000 genomes]
rs684680	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-11995600	Weak transcription	Primary T cells from cord blood	blood
3	chr18:11982600-11995800	Weak transcription	Thymus	Thymus
4	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
5	chr18:11983400-11994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:11984200-11994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:11984400-11994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:11984400-11994200	Weak transcription	NHEK	skin
9	chr18:11984400-11995000	Weak transcription	GM12878-XiMat	blood
10	chr18:11986000-11995600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr18:11986400-11994600	Weak transcription	Liver	Liver
12	chr18:11987200-11994800	Weak transcription	Right Atrium	heart
13	chr18:11988000-11995600	Weak transcription	K562	blood
14	chr18:11988600-11995200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr18:11988800-11994200	Weak transcription	Adipose Nuclei	Adipose
16	chr18:11989400-11994400	Enhancers	HepG2	liver
17	chr18:11989400-11994600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr18:11989600-11996400	Enhancers	Pancreas	Pancrea
19	chr18:11989800-11994600	Weak transcription	Left Ventricle	heart
20	chr18:11990000-11994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:11990000-11994400	Weak transcription	Colonic Mucosa	Colon
22	chr18:11990000-11994800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr18:11990200-11995200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr18:11990400-11994400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr18:11990400-11994400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr18:11990400-11994600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr18:11990400-11994600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr18:11990400-11994600	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr18:11990600-11994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:11990600-11994600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:11990600-11995800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr18:11990800-11994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr18:11990800-11994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr18:11990800-11994600	Weak transcription	NHLF	lung
35	chr18:11990800-11994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:11990800-11994800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr18:11990800-11995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr18:11991000-11994400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:11991000-11994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr18:11991000-11995200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr18:11991000-11999200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr18:11991200-11993800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr18:11991200-11994200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr18:11991200-11994400	Weak transcription	Fetal Lung	lung
45	chr18:11991200-11994800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:11991400-11994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr18:11991400-11994600	Strong transcription	Fetal Stomach	stomach
48	chr18:11991600-11993800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr18:11991600-11993800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr18:11991600-11994200	Weak transcription	HSMM	muscle

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