Variant report

Variant	rs17030451
Chromosome Location	chr1:113064374-113064375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113064315-113064453	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113062631..113064909-chr1:113068570..113071113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273483	TF binding region
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10399919	0.83[AFR][1000 genomes]
rs11102490	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102492	1.00[AMR][1000 genomes]
rs11102500	0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060267	0.92[AFR][1000 genomes]
rs12069022	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069740	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12073750	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs12077330	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs12080006	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082350	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12087862	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs12091635	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094504	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030446	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030455	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030475	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030592	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs4424506	0.84[YRI][hapmap]
rs58634778	0.83[AFR][1000 genomes]
rs59324334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984503	0.83[AFR][1000 genomes]
rs72993070	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993072	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:113052200-113067600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:113052400-113067000	Weak transcription	Adipose Nuclei	Adipose
5	chr1:113054600-113066800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:113055000-113067000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:113055800-113067200	Weak transcription	Fetal Lung	lung
8	chr1:113055800-113067600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
10	chr1:113056000-113067600	Weak transcription	HUVEC	blood vessel
11	chr1:113056600-113066800	Weak transcription	Placenta	Placenta
12	chr1:113057000-113067000	Weak transcription	Colonic Mucosa	Colon
13	chr1:113057600-113067000	Weak transcription	Fetal Brain Female	brain
14	chr1:113057800-113066800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:113057800-113067600	Weak transcription	Fetal Intestine Large	intestine
16	chr1:113057800-113069600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:113058200-113067400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:113058400-113065400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:113058400-113069600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:113058400-113086600	Weak transcription	A549	lung
21	chr1:113058600-113064800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:113058600-113065800	Strong transcription	Fetal Stomach	stomach
23	chr1:113058600-113067400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:113058600-113069400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:113058800-113064800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:113058800-113067200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:113058800-113119400	Weak transcription	HepG2	liver
28	chr1:113059000-113064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:113059000-113064800	Weak transcription	NHLF	lung
30	chr1:113059000-113065200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:113059000-113067000	Weak transcription	Right Ventricle	heart
32	chr1:113059200-113067600	Weak transcription	Primary T cells from cord blood	blood
33	chr1:113059200-113071600	Weak transcription	Hela-S3	cervix
34	chr1:113059600-113069600	Weak transcription	Spleen	Spleen
35	chr1:113060000-113065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:113060200-113064800	Weak transcription	Lung	lung
37	chr1:113060200-113065000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:113060200-113067000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:113060200-113067000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:113060200-113067200	Weak transcription	Gastric	stomach
41	chr1:113060200-113069600	Weak transcription	Aorta	Aorta
42	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
43	chr1:113060400-113065200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:113060400-113067000	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:113060400-113067400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:113060400-113070400	Weak transcription	HMEC	breast
47	chr1:113060800-113067600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:113061000-113064800	Weak transcription	NHEK	skin
49	chr1:113061000-113067600	Weak transcription	Esophagus	oesophagus
50	chr1:113061200-113072200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links