Variant report

Variant	rs6561648
Chromosome Location	chr13:52399805-52399806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52387973..52389920-chr13:52398590..52400891,2	K562	blood:
2	chr13:52389100..52392374-chr13:52395474..52400602,4	MCF-7	breast:
3	chr13:52122493..52124445-chr13:52397766..52400689,2	K562	blood:
4	chr13:52387525..52389920-chr13:52398590..52400891,3	K562	blood:
5	chr13:52398927..52403579-chr13:52421576..52424929,4	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs520968	1.00[ASN][1000 genomes]
rs619869	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6561649	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52392400-52404800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:52392800-52401800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr13:52393600-52406200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:52393600-52418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:52393800-52400000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:52394600-52400200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:52396000-52400000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:52396600-52400400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:52396600-52404000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr13:52396600-52404600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:52397000-52400200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:52397400-52400400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:52397600-52400600	Weak transcription	Spleen	Spleen
14	chr13:52397800-52400000	Active TSS	Primary T cells from cord blood	blood
15	chr13:52398000-52400800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr13:52398000-52401000	Enhancers	HSMMtube	muscle
17	chr13:52398000-52404400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr13:52398200-52404200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr13:52398400-52400600	Weak transcription	Brain Hippocampus Middle	brain
20	chr13:52398400-52401600	Enhancers	Primary B cells from peripheral blood	blood
21	chr13:52398600-52400200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:52398600-52401000	Weak transcription	Fetal Stomach	stomach
23	chr13:52398600-52402200	Enhancers	Colon Smooth Muscle	Colon
24	chr13:52398600-52402800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr13:52398800-52400000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr13:52398800-52400800	Weak transcription	Brain Substantia Nigra	brain
27	chr13:52398800-52404600	Enhancers	Primary hematopoietic stem cells	blood
28	chr13:52399000-52400000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr13:52399000-52400200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:52399000-52400200	Enhancers	Dnd41	blood
31	chr13:52399000-52400600	Enhancers	Stomach Smooth Muscle	stomach
32	chr13:52399000-52400800	Enhancers	GM12878-XiMat	blood
33	chr13:52399000-52402200	Enhancers	Fetal Muscle Leg	muscle
34	chr13:52399200-52400000	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr13:52399200-52400200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:52399200-52400200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:52399200-52400400	Weak transcription	Colonic Mucosa	Colon
38	chr13:52399200-52402400	Enhancers	Fetal Heart	heart
39	chr13:52399400-52400200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr13:52399400-52400400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr13:52399400-52400800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr13:52399400-52401200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr13:52399400-52401200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr13:52399400-52401400	Enhancers	Rectal Smooth Muscle	rectum
45	chr13:52399400-52401600	Enhancers	Brain Anterior Caudate	brain
46	chr13:52399400-52402600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr13:52399400-52404600	Enhancers	Fetal Thymus	thymus
48	chr13:52399600-52400000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr13:52399600-52400400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr13:52399600-52401000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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