Variant report

Variant	rs1390402
Chromosome Location	chr1:227798053-227798054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227797816..227799614-chr1:227803015..227804639,2	MCF-7	breast:
2	chr1:227786695..227788345-chr1:227795346..227798093,2	K562	blood:
3	chr1:227797075..227799559-chr1:227811537..227814521,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225934	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10159323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10916168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1587156	0.80[AFR][1000 genomes]
rs1817929	1.00[AMR][1000 genomes]
rs1826774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1874372	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2313246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2492633	1.00[AMR][1000 genomes]
rs2644142	1.00[AMR][1000 genomes]
rs2814062	1.00[AMR][1000 genomes]
rs2819497	1.00[AMR][1000 genomes]
rs2935148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2935150	0.80[AFR][1000 genomes]
rs2935151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2999738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2999739	1.00[AFR][1000 genomes]
rs2999747	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3010184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4653513	1.00[AMR][1000 genomes]
rs6426466	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6426467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662898	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7521659	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7540705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs903696	1.00[AMR][1000 genomes]
rs976960	1.00[AMR][1000 genomes]
rs9943170	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227774800-227799200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:227779200-227799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:227781200-227800800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:227784000-227798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:227784000-227799600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:227790800-227801800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:227791000-227799600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:227791400-227798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:227791400-227798200	Weak transcription	Gastric	stomach
13	chr1:227791400-227799200	Weak transcription	Ovary	ovary
14	chr1:227791400-227799600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:227791400-227801000	Weak transcription	Psoas Muscle	Psoas
16	chr1:227792000-227798800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:227792600-227799600	Weak transcription	Thymus	Thymus
18	chr1:227792800-227798400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:227794400-227804400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:227794600-227800000	Weak transcription	Right Ventricle	heart
21	chr1:227794600-227802000	Weak transcription	Placenta	Placenta
22	chr1:227794600-227808600	Weak transcription	Left Ventricle	heart
23	chr1:227795200-227801200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:227795200-227807000	Weak transcription	Fetal Heart	heart
25	chr1:227795400-227798200	Weak transcription	Primary B cells from cord blood	blood
26	chr1:227796200-227807200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:227796600-227799600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:227796800-227801600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:227796800-227806000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:227797400-227799000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:227797400-227799800	Weak transcription	HSMMtube	muscle
32	chr1:227797400-227803400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:227797600-227799400	Weak transcription	Brain Substantia Nigra	brain
34	chr1:227797600-227804800	ZNF genes & repeats	Fetal Stomach	stomach
35	chr1:227797800-227798400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:227797800-227799200	Weak transcription	Fetal Intestine Large	intestine
37	chr1:227797800-227800400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:227797800-227800400	ZNF genes & repeats	Dnd41	blood
39	chr1:227797800-227804800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:227797800-227805800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr1:227797800-227806400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
42	chr1:227797800-227807200	ZNF genes & repeats	Fetal Brain Female	brain
43	chr1:227798000-227798400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:227798000-227798400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:227798000-227799200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr1:227798000-227799400	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr1:227798000-227799600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:227798000-227799800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr1:227798000-227800600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:227798000-227800600	Weak transcription	HUVEC	blood vessel

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