Variant report

Variant	rs56049309
Chromosome Location	chr6:26311330-26311331
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26310739..26313111-chr6:26519898..26523183,4	K562	blood:
2	chr6:26310563..26314155-chr6:26536895..26540158,5	K562	blood:
3	chr6:26309632..26313347-chr6:27114067..27115956,3	MCF-7	breast:
4	chr6:26310464..26312772-chr6:27099903..27102322,2	MCF-7	breast:
5	chr6:26309822..26312152-chr6:27114405..27116327,2	MCF-7	breast:
6	chr6:26309646..26311528-chr6:26321408..26324123,2	MCF-7	breast:
7	chr6:26309854..26311827-chr6:30584744..30586580,2	K562	blood:
8	chr6:26295127..26298066-chr6:26310919..26313160,2	MCF-7	breast:
9	chr6:26311313..26315619-chr6:26320947..26324621,7	MCF-7	breast:
10	chr6:26311071..26313329-chr6:26552209..26554429,3	K562	blood:
11	chr6:26305172..26308456-chr6:26309318..26312208,7	MCF-7	breast:
12	chr6:26308793..26311615-chr6:26576648..26578287,2	K562	blood:
13	chr6:26310371..26313077-chr6:26554610..26556744,3	K562	blood:
14	chr6:26310739..26313119-chr6:26520037..26523183,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000220875	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000196787	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs16891646	1.00[EUR][1000 genomes]
rs16891681	1.00[EUR][1000 genomes]
rs2393651	1.00[EUR][1000 genomes]
rs3846850	1.00[EUR][1000 genomes]
rs41266825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55674533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56973463	1.00[AMR][1000 genomes]
rs59620817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397366	1.00[EUR][1000 genomes]
rs73736553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736555	1.00[EUR][1000 genomes]
rs73736558	1.00[AMR][1000 genomes]
rs73736559	1.00[EUR][1000 genomes]
rs73736560	1.00[EUR][1000 genomes]
rs73736561	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736562	1.00[EUR][1000 genomes]
rs73736566	1.00[EUR][1000 genomes]
rs73736574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736578	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736580	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736581	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73736582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
8	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
9	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases
10	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 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	chr6:26305600-26311400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:26305600-26313400	Weak transcription	Small Intestine	intestine
3	chr6:26305800-26311600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:26305800-26312000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:26305800-26312400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:26306200-26311600	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:26306200-26311600	Weak transcription	Placenta	Placenta
8	chr6:26306200-26311600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:26306200-26311800	Weak transcription	Fetal Lung	lung
10	chr6:26306200-26312000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:26306400-26311600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:26306400-26311600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:26306400-26312000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:26306800-26311800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:26307600-26312200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:26308400-26311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:26308400-26311800	Weak transcription	Dnd41	blood
18	chr6:26308600-26311600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:26308600-26311600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:26308600-26312000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:26308600-26312200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:26308600-26313000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:26309400-26314200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:26309600-26311400	Flanking Active TSS	K562	blood
25	chr6:26309600-26311600	Enhancers	Fetal Intestine Large	intestine
26	chr6:26309800-26311600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:26309800-26311600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:26310200-26311600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:26310200-26311600	Enhancers	Fetal Intestine Small	intestine
30	chr6:26310400-26311400	Flanking Active TSS	HepG2	liver
31	chr6:26310400-26311800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:26310400-26311800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:26310600-26311600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:26310600-26311600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr6:26310600-26311600	Weak transcription	HSMMtube	muscle
36	chr6:26310600-26311800	Weak transcription	HSMM	muscle
37	chr6:26310600-26314400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:26310600-26314400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:26310800-26311400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:26310800-26311600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:26310800-26311800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:26310800-26311800	Weak transcription	Liver	Liver
43	chr6:26310800-26311800	Weak transcription	Psoas Muscle	Psoas
44	chr6:26310800-26312000	Enhancers	Primary T cells fromperipheralblood	blood
45	chr6:26310800-26312000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:26310800-26314200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:26310800-26314200	Active TSS	Fetal Muscle Trunk	muscle
48	chr6:26310800-26314400	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr6:26310800-26314600	Active TSS	H1 Cell Line	embryonic stem cell
50	chr6:26311000-26311400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links