Variant report

Variant	rs17118430
Chromosome Location	chr1:59395828-59395829
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59244053..59249750-chr1:59393075..59399809,12	K562	blood:
2	chr1:59390738..59393434-chr1:59395453..59397807,2	MCF-7	breast:
3	chr1:59392641..59396388-chr1:59399124..59401431,3	K562	blood:
4	chr1:59246732..59251125-chr1:59394532..59399253,8	MCF-7	breast:
5	chr1:59244308..59248659-chr1:59395754..59399809,6	K562	blood:
6	chr1:59245645..59251479-chr1:59393366..59398471,10	MCF-7	breast:
7	chr1:59280123..59281954-chr1:59395680..59397207,2	MCF-7	breast:
8	chr1:59284595..59286940-chr1:59394772..59397437,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11806596	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118423	0.81[EUR][1000 genomes]
rs17118441	0.86[EUR][1000 genomes]
rs1886744	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2477743	0.81[EUR][1000 genomes]
rs55834295	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56040345	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56175432	0.82[EUR][1000 genomes]
rs56251271	0.81[EUR][1000 genomes]
rs58558886	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66555203	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681035	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72678896	0.82[EUR][1000 genomes]
rs72678899	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72678900	0.81[EUR][1000 genomes]
rs72678901	0.80[AMR][1000 genomes];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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59385200-59397800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:59386600-59399800	Enhancers	Fetal Intestine Small	intestine
3	chr1:59388400-59397800	Weak transcription	NHLF	lung
4	chr1:59388600-59397800	Weak transcription	Lung	lung
5	chr1:59388800-59397800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:59388800-59398600	Weak transcription	Pancreas	Pancrea
7	chr1:59389000-59398800	Weak transcription	Right Atrium	heart
8	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
9	chr1:59389200-59398600	Weak transcription	Psoas Muscle	Psoas
10	chr1:59389200-59401400	Weak transcription	Left Ventricle	heart
11	chr1:59390200-59399600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:59391200-59399600	Enhancers	Fetal Intestine Large	intestine
13	chr1:59391600-59396200	Enhancers	Duodenum Mucosa	Duodenum
14	chr1:59391800-59396600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:59392000-59397800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:59392000-59399600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:59392600-59396200	Enhancers	HMEC	breast
18	chr1:59392600-59398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:59392600-59399400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:59393000-59396000	Enhancers	K562	blood
21	chr1:59393200-59398400	Weak transcription	Adipose Nuclei	Adipose
22	chr1:59393400-59397600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:59393400-59398800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:59393600-59397600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:59393600-59398600	Weak transcription	Fetal Lung	lung
26	chr1:59393600-59400800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:59393600-59406800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:59393800-59396000	Flanking Active TSS	Hela-S3	cervix
29	chr1:59393800-59398600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:59394400-59396200	Bivalent Enhancer	HepG2	liver
31	chr1:59394400-59396600	Enhancers	Small Intestine	intestine
32	chr1:59394600-59396000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:59394600-59396400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:59394800-59396000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:59395000-59396000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:59395000-59396000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:59395000-59396200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:59395000-59396400	Enhancers	Primary T cells from cord blood	blood
39	chr1:59395000-59397600	Enhancers	Stomach Mucosa	stomach
40	chr1:59395200-59396000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:59395200-59396000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:59395200-59396000	Enhancers	Esophagus	oesophagus
43	chr1:59395200-59396200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr1:59395400-59396000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr1:59395400-59396000	Enhancers	Fetal Thymus	thymus
46	chr1:59395400-59398400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:59395400-59398600	Weak transcription	Gastric	stomach
48	chr1:59395400-59398800	Enhancers	NHEK	skin
49	chr1:59395600-59396000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr1:59395600-59396000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links