Variant report

Variant	rs16842062
Chromosome Location	chr1:223908780-223908781
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223907255..223908800-chr1:223930400..223932243,2	MCF-7	breast:
2	chr1:223907922..223910776-chr1:223912986..223915507,4	MCF-7	breast:
3	chr1:223906267..223909049-chr1:223925924..223927616,2	MCF-7	breast:
4	chr1:223907382..223910369-chr1:223910890..223914136,6	MCF-7	breast:
5	chr1:223907868..223910844-chr1:223920862..223922625,2	K562	blood:
6	chr1:223907966..223910136-chr1:223920421..223923104,3	K562	blood:
7	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
8	chr1:223893339..223895149-chr1:223908557..223910552,2	K562	blood:
9	chr1:223908483..223912094-chr1:223930572..223933646,3	MCF-7	breast:
10	chr1:223907649..223910322-chr1:223936946..223940552,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10916601	0.82[ASN][1000 genomes]
rs10916602	0.82[ASN][1000 genomes]
rs11579787	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580689	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581716	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588475	0.90[EUR][1000 genomes]
rs12074091	0.82[ASN][1000 genomes]
rs12080565	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1539707	0.91[ASN][1000 genomes]
rs16842040	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1892077	0.82[ASN][1000 genomes]
rs2154113	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2186006	0.82[ASN][1000 genomes]
rs2275877	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370012	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370013	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28370014	0.82[ASN][1000 genomes]
rs28370020	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28370029	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653499	0.82[ASN][1000 genomes]
rs61823966	0.82[ASN][1000 genomes]
rs6669046	0.96[ASN][1000 genomes]
rs6674733	0.95[ASN][1000 genomes]
rs7366009	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7414311	0.82[ASN][1000 genomes]
rs7555491	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223903400-223908800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:223903600-223909400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:223904000-223909000	Genic enhancers	Hela-S3	cervix
9	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
10	chr1:223904200-223909800	Genic enhancers	NH-A	brain
11	chr1:223904400-223910000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:223904400-223922400	Genic enhancers	NHLF	lung
14	chr1:223904600-223909800	Genic enhancers	HUVEC	blood vessel
15	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
16	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
17	chr1:223904800-223909000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:223904800-223909000	Strong transcription	Brain Angular Gyrus	brain
19	chr1:223904800-223909200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr1:223904800-223909400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:223904800-223909400	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr1:223904800-223909600	Genic enhancers	HSMM	muscle
23	chr1:223904800-223910600	Genic enhancers	Muscle Satellite Cultured Cells	--
24	chr1:223904800-223911800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:223904800-223913200	Strong transcription	Fetal Stomach	stomach
26	chr1:223904800-223914000	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr1:223905000-223909200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:223905000-223911600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:223905200-223909000	Strong transcription	Esophagus	oesophagus
30	chr1:223905200-223909400	Strong transcription	Brain Germinal Matrix	brain
31	chr1:223905200-223911400	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:223905400-223909600	Strong transcription	Fetal Brain Female	brain
33	chr1:223905600-223909600	Genic enhancers	HSMMtube	muscle
34	chr1:223905600-223910800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:223905600-223910800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:223905600-223912200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:223905600-223912400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:223906000-223909000	Strong transcription	Lung	lung
39	chr1:223906000-223909800	Genic enhancers	Fetal Intestine Small	intestine
40	chr1:223906000-223913800	Weak transcription	Primary B cells from cord blood	blood
41	chr1:223906200-223909000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:223906200-223909400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:223906200-223909800	Genic enhancers	Fetal Intestine Large	intestine
44	chr1:223906200-223913000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr1:223906200-223915600	Weak transcription	Aorta	Aorta
46	chr1:223906400-223909200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:223906400-223909200	Enhancers	HepG2	liver
48	chr1:223906400-223909800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:223906400-223910800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr1:223906400-223913600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links