Variant report

Variant	rs2859353
Chromosome Location	chr6:28456855-28456856
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28446745..28449657-chr6:28455146..28458037,3	MCF-7	breast:
2	chr6:27858756..27861228-chr6:28455818..28458096,2	K562	blood:
3	chr6:28372326..28375748-chr6:28455628..28458983,4	K562	blood:
4	chr6:28456446..28459153-chr6:28555326..28557057,2	MCF-7	breast:
5	chr6:28187359..28189911-chr6:28455377..28457870,2	K562	blood:
6	chr6:28451721..28454293-chr6:28455250..28457902,2	MCF-7	breast:
7	chr6:28455757..28458631-chr6:28484303..28486741,3	K562	blood:
8	chr19:27731802..27732517-chr6:28456742..28457568,2	NB4	blood:
9	chr6:28456451..28458356-chr6:28686774..28688606,2	K562	blood:
10	chr6:28456855..28459742-chr6:28553402..28555898,3	MCF-7	breast:
11	chr6:28364266..28370257-chr6:28453674..28463075,14	K562	blood:
12	chr6:28455752..28457337-chr6:28581196..28584117,2	K562	blood:
13	chr6:28188045..28189911-chr6:28456370..28458760,2	K562	blood:
14	chr6:28192543..28195348-chr6:28455724..28457783,2	K562	blood:
15	chr6:28455084..28458229-chr6:28499553..28502958,3	K562	blood:
16	chr6:28364227..28369783-chr6:28455559..28460332,7	K562	blood:
17	chr6:27858485..27861228-chr6:28455818..28458807,3	K562	blood:
18	chr6:28446299..28448037-chr6:28455509..28457029,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000246350	Chromatin interaction
ENSG00000158691	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015810	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11965542	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11966042	0.82[EUR][1000 genomes]
rs11966237	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11968771	0.83[ASN][1000 genomes]
rs11969150	0.82[EUR][1000 genomes]
rs11969304	0.83[ASN][1000 genomes]
rs11970404	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2078422	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213235	0.82[EUR][1000 genomes]
rs2159274	0.90[EUR][1000 genomes]
rs2531801	0.82[EUR][1000 genomes]
rs2531802	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2531812	0.90[EUR][1000 genomes]
rs2531816	0.82[EUR][1000 genomes]
rs2531818	0.86[AFR][1000 genomes]
rs2531819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2531826	0.82[EUR][1000 genomes]
rs2531828	0.82[EUR][1000 genomes]
rs28382592	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2859349	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2859350	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2859354	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2859359	0.82[EUR][1000 genomes]
rs2859362	0.82[EUR][1000 genomes]
rs2859367	0.82[EUR][1000 genomes]
rs2859371	0.90[EUR][1000 genomes]
rs2859376	0.90[EUR][1000 genomes]
rs2859377	0.90[EUR][1000 genomes]
rs2859378	0.90[EUR][1000 genomes]
rs385908	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs400987	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs403774	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs423118	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59457415	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61540948	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62638680	0.82[EUR][1000 genomes]
rs6916243	0.82[EUR][1000 genomes]
rs6932394	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs719370	0.82[EUR][1000 genomes]
rs73385806	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73385807	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73385810	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73385818	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73385870	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73387810	0.82[EUR][1000 genomes]
rs73391136	0.83[ASN][1000 genomes]
rs73399084	0.82[EUR][1000 genomes]
rs73401012	0.82[EUR][1000 genomes]
rs73401666	0.82[EUR][1000 genomes]
rs73407126	0.83[ASN][1000 genomes]
rs73409123	0.83[ASN][1000 genomes]
rs73409134	0.83[ASN][1000 genomes]
rs7739389	0.82[EUR][1000 genomes]
rs7759845	0.82[EUR][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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28455200-28457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28456400-28457000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr6:28456400-28457800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:28456400-28458000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:28456400-28458200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:28456400-28458200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:28456400-28458400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:28456400-28459400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:28456400-28460200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:28456600-28457000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:28456600-28457000	Flanking Active TSS	Fetal Lung	lung
12	chr6:28456600-28457000	Enhancers	Placenta	Placenta
13	chr6:28456600-28457000	Bivalent Enhancer	Thymus	Thymus
14	chr6:28456600-28457200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
15	chr6:28456600-28457400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr6:28456600-28457600	Active TSS	Brain Angular Gyrus	brain
17	chr6:28456600-28458200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:28456600-28458200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:28456600-28458400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr6:28456600-28458400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:28456600-28458400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:28456600-28458400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr6:28456600-28458600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:28456600-28458600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:28456600-28458600	Active TSS	Ovary	ovary
26	chr6:28456600-28458800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:28456600-28458800	Active TSS	A549	lung
28	chr6:28456600-28458800	Active TSS	GM12878-XiMat	blood
29	chr6:28456800-28457000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:28456800-28457000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:28456800-28457000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr6:28456800-28457000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
33	chr6:28456800-28457000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
34	chr6:28456800-28457000	Bivalent/Poised TSS	Fetal Brain Male	brain
35	chr6:28456800-28457000	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
36	chr6:28456800-28457000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr6:28456800-28457000	Flanking Active TSS	HepG2	liver
38	chr6:28456800-28457000	Flanking Active TSS	HMEC	breast
39	chr6:28456800-28457200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr6:28456800-28457200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
41	chr6:28456800-28457200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:28456800-28457200	Flanking Active TSS	HUVEC	blood vessel
43	chr6:28456800-28457600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:28456800-28457600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr6:28456800-28457600	Active TSS	NHEK	skin
46	chr6:28456800-28457800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:28456800-28457800	Active TSS	Brain Anterior Caudate	brain
48	chr6:28456800-28457800	Active TSS	NH-A	brain
49	chr6:28456800-28458000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:28456800-28458000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links