Variant report

Variant	rs13220596
Chromosome Location	chr6:24645675-24645676
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24644992..24647314-chr6:24719656..24721157,2	MCF-7	breast:
2	chr6:24645396..24648521-chr6:24658092..24661192,3	K562	blood:
3	chr6:24645218..24647641-chr6:24665331..24668427,5	MCF-7	breast:
4	chr6:24645396..24648552-chr6:24658188..24661192,4	K562	blood:
5	chr6:24645670..24648708-chr6:24654981..24659486,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111802	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10456043	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456312	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759149	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195384	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213672	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34211261	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv601164	chr6:24625091-24661599	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv601165	chr6:24632642-24666007	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24643600-24647000	Active TSS	Fetal Brain Female	brain
2	chr6:24644000-24646800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr6:24644000-24647000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:24644200-24647000	Active TSS	Brain Anterior Caudate	brain
5	chr6:24644400-24645800	Weak transcription	Gastric	stomach
6	chr6:24644600-24645800	Active TSS	Fetal Brain Male	brain
7	chr6:24644600-24645800	Weak transcription	Lung	lung
8	chr6:24645400-24645800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:24645400-24645800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:24645400-24646000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:24645400-24646000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
12	chr6:24645400-24646000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:24645400-24647000	Active TSS	Brain Angular Gyrus	brain
14	chr6:24645600-24645800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:24645600-24645800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:24645600-24645800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:24645600-24645800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr6:24645600-24645800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
19	chr6:24645600-24645800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:24645600-24645800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
21	chr6:24645600-24645800	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:24645600-24645800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
23	chr6:24645600-24645800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
24	chr6:24645600-24645800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:24645600-24645800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:24645600-24645800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:24645600-24645800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:24645600-24645800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
29	chr6:24645600-24645800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:24645600-24645800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:24645600-24645800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
32	chr6:24645600-24645800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr6:24645600-24645800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr6:24645600-24645800	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr6:24645600-24645800	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr6:24645600-24645800	Enhancers	Right Ventricle	heart
37	chr6:24645600-24645800	Enhancers	Spleen	Spleen
38	chr6:24645600-24645800	Enhancers	HMEC	breast
39	chr6:24645600-24645800	Bivalent Enhancer	HUVEC	blood vessel
40	chr6:24645600-24645800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
41	chr6:24645600-24645800	Enhancers	NH-A	brain
42	chr6:24645600-24646000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
43	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:24645600-24646000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:24645600-24646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:24645600-24646000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr6:24645600-24646000	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:24645600-24646000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:24645600-24646000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links