Variant report

Variant	rs57342039
Chromosome Location	chr1:228416158-228416159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228407306..228411999-chr1:228412295..228416286,6	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12060771	0.94[AFR][1000 genomes]
rs3845621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57278773	1.00[AFR][1000 genomes]
rs57986391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59850477	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60200244	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60639760	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60648546	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6656212	1.00[AMR][1000 genomes]
rs6676755	1.00[AMR][1000 genomes]
rs6704220	1.00[AMR][1000 genomes]
rs9728319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228402200-228425800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:228402200-228428800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:228402600-228418000	Strong transcription	Primary T cells from cord blood	blood
4	chr1:228403000-228428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:228403200-228418000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:228410000-228416600	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr1:228410600-228416400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:228410800-228416800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:228411600-228416800	Strong transcription	Dnd41	blood
10	chr1:228411800-228416200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:228411800-228416400	Weak transcription	K562	blood
12	chr1:228411800-228417000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:228411800-228420200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:228412000-228416800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr1:228412400-228420400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:228412600-228420800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:228412800-228416800	Strong transcription	Fetal Thymus	thymus
18	chr1:228413000-228416200	Strong transcription	Thymus	Thymus
19	chr1:228413000-228416800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:228413000-228425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:228413000-228426000	Weak transcription	Right Atrium	heart
22	chr1:228413000-228428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:228413000-228428800	Weak transcription	Gastric	stomach
24	chr1:228413200-228417000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:228413200-228417000	Strong transcription	Fetal Brain Female	brain
26	chr1:228413200-228418200	Weak transcription	Fetal Kidney	kidney
27	chr1:228413200-228420200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:228413200-228422400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:228413200-228424400	Weak transcription	Brain Anterior Caudate	brain
30	chr1:228413200-228426200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:228413400-228416200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:228413400-228416600	Strong transcription	Brain Germinal Matrix	brain
33	chr1:228413400-228417200	Strong transcription	Fetal Lung	lung
34	chr1:228413400-228421000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:228413400-228426000	Weak transcription	Fetal Brain Male	brain
36	chr1:228413600-228416200	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:228413600-228416200	Strong transcription	Fetal Stomach	stomach
38	chr1:228413600-228417200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:228413600-228418400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:228413600-228419200	Weak transcription	HSMMtube	muscle
41	chr1:228413600-228420400	Weak transcription	Primary B cells from cord blood	blood
42	chr1:228413600-228422200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:228413600-228428800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:228413800-228417800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:228413800-228428600	Weak transcription	Pancreas	Pancrea
46	chr1:228413800-228429000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:228414000-228416200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:228414000-228419600	Weak transcription	A549	lung
49	chr1:228414000-228419800	Weak transcription	Fetal Heart	heart
50	chr1:228414200-228417800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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