Variant report

Variant	rs2747677
Chromosome Location	chr6:24904676-24904677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2064524	0.92[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2207399	0.82[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747674	0.82[ASN][1000 genomes]
rs2747675	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2747676	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2747683	0.91[CHB][hapmap]
rs2817718	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2817722	0.90[CHB][hapmap]
rs2817723	0.82[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs2817725	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2817726	0.86[ASN][1000 genomes]
rs2817727	0.88[ASN][1000 genomes]
rs2817731	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2817733	0.82[ASN][1000 genomes]
rs734014	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs734015	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs932494	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24884000-24908200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:24891600-24908400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:24896400-24908600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr6:24897400-24904800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:24897400-24907600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:24897400-24909600	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr6:24899000-24908200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:24899800-24909600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:24900000-24906000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:24900000-24909000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr6:24900200-24909800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:24900400-24907800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:24900400-24908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:24900400-24908200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:24900400-24908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:24900600-24905600	Weak transcription	Brain Anterior Caudate	brain
17	chr6:24900600-24907200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:24900600-24907600	Weak transcription	Fetal Heart	heart
19	chr6:24900800-24905400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:24901000-24908800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:24901800-24907800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:24901800-24908000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:24901800-24908800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:24902000-24905600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:24902000-24907800	Weak transcription	GM12878-XiMat	blood
26	chr6:24902200-24907600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:24902200-24909400	Weak transcription	Left Ventricle	heart
28	chr6:24902400-24905200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:24902400-24905800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr6:24902400-24907800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:24903200-24904800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:24903200-24906400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:24903200-24906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:24903400-24905400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:24903400-24905800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:24903600-24906400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr6:24903600-24908600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:24903600-24908800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:24903800-24905400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:24903800-24906200	Strong transcription	Primary B cells from cord blood	blood
41	chr6:24904000-24904800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:24904000-24904800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr6:24904000-24905000	ZNF genes & repeats	Aorta	Aorta
44	chr6:24904000-24905000	Strong transcription	Spleen	Spleen
45	chr6:24904000-24905200	Strong transcription	Primary hematopoietic stem cells	blood
46	chr6:24904200-24905000	Enhancers	Fetal Muscle Leg	muscle
47	chr6:24904200-24905400	Weak transcription	NHDF-Ad	bronchial
48	chr6:24904200-24907800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:24904200-24908200	Weak transcription	Dnd41	blood
50	chr6:24904400-24905200	Strong transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links