Variant report

Variant	rs6115256
Chromosome Location	chr20:25666642-25666643
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	chr20:25666393..25667340-chr20:25675280..25676053,2	MCF-7	breast:
2	chr20:25603625..25606406-chr20:25665177..25670447,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NANP-1	chr20:25666632-25666885	NONHSAT079178

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10470065	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17244452	0.94[AFR][1000 genomes]
rs55652038	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56184302	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6107071	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6115208	0.84[AFR][1000 genomes]
rs6115211	0.88[AFR][1000 genomes]
rs6115223	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6115248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102106	0.83[EUR][1000 genomes]
rs73102113	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73102121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73111222	0.89[EUR][1000 genomes]
rs73111242	0.82[AFR][1000 genomes]
rs73113144	0.94[AFR][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	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25656600-25667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr20:25657200-25667200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:25657200-25674200	Weak transcription	Fetal Heart	heart
4	chr20:25657400-25676200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr20:25657600-25667200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:25657600-25672200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr20:25657600-25672600	Weak transcription	Fetal Brain Male	brain
8	chr20:25657600-25676000	Weak transcription	Stomach Mucosa	stomach
9	chr20:25657600-25676200	Weak transcription	Hela-S3	cervix
10	chr20:25657600-25676200	Weak transcription	K562	blood
11	chr20:25657600-25676400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr20:25657800-25667000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:25657800-25667200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:25657800-25676000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr20:25657800-25676200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr20:25657800-25676200	Weak transcription	Colonic Mucosa	Colon
17	chr20:25657800-25676200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr20:25658000-25667200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr20:25658200-25676200	Weak transcription	Fetal Kidney	kidney
20	chr20:25658400-25676200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr20:25658800-25676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr20:25659000-25676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr20:25659600-25667600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:25660600-25676000	Weak transcription	HUVEC	blood vessel
25	chr20:25662200-25672000	Weak transcription	NH-A	brain
26	chr20:25662400-25676000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr20:25662600-25672200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:25662800-25672000	Weak transcription	Primary B cells from cord blood	blood
29	chr20:25663800-25676000	Weak transcription	HMEC	breast
30	chr20:25664000-25667000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr20:25664000-25675600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr20:25664000-25676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr20:25664000-25676000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr20:25664200-25672000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr20:25664200-25675200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr20:25664200-25676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr20:25665000-25667400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr20:25665200-25666800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr20:25665200-25667000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr20:25665200-25667000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:25665200-25667000	Strong transcription	Fetal Lung	lung
42	chr20:25665200-25667200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:25665200-25667200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:25665200-25667200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr20:25665200-25667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr20:25665200-25667600	Strong transcription	Adipose Nuclei	Adipose
47	chr20:25665400-25667200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr20:25665400-25667400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:25665400-25667400	Strong transcription	A549	lung
50	chr20:25665400-25667400	Strong transcription	HepG2	liver

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