Variant report

Variant	rs13129679
Chromosome Location	chr4:2576102-2576103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2570913..2572665-chr4:2576002..2578236,2	MCF-7	breast:
2	chr4:2546552..2548542-chr4:2575519..2578316,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13111143	1.00[ASW][hapmap]
rs13121085	1.00[ASW][hapmap]
rs13125136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13138097	1.00[CHB][hapmap]
rs13152126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17629977	1.00[CHB][hapmap]
rs17681870	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs17697511	1.00[CHB][hapmap]
rs17773510	1.00[CHB][hapmap]
rs17774505	1.00[CHB][hapmap]
rs17824109	1.00[CHB][hapmap]
rs17824295	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs34218188	1.00[ASW][hapmap];1.00[CHB][hapmap]
rs34574967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35224370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35546272	0.81[EUR][1000 genomes]
rs35670376	1.00[AMR][1000 genomes]
rs6836434	1.00[CHB][hapmap]
rs71608203	1.00[AFR][1000 genomes]
rs71608205	1.00[AFR][1000 genomes]
rs71608211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71608217	1.00[AFR][1000 genomes]
rs71608219	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7340951	1.00[CHB][hapmap]

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	nsv432548	chr4:1725009-2652494	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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 miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv1003409	chr4:2541224-2724199	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2540000-2585200	Weak transcription	Osteobl	bone
2	chr4:2540400-2576600	Weak transcription	NHLF	lung
3	chr4:2545200-2585000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:2548400-2584200	Weak transcription	A549	lung
5	chr4:2551000-2584400	Weak transcription	NHEK	skin
6	chr4:2559200-2590800	Weak transcription	Fetal Kidney	kidney
7	chr4:2559800-2584800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:2560400-2581400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:2562000-2588800	Weak transcription	NHDF-Ad	bronchial
10	chr4:2562600-2584000	Weak transcription	NH-A	brain
11	chr4:2562800-2584600	Weak transcription	Hela-S3	cervix
12	chr4:2565200-2576200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:2565400-2576800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:2565600-2584800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:2566000-2584400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:2567800-2584600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:2568400-2580800	Weak transcription	Fetal Intestine Large	intestine
18	chr4:2568600-2584200	Weak transcription	Fetal Heart	heart
19	chr4:2569200-2576200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:2570400-2582000	Weak transcription	Placenta	Placenta
21	chr4:2570600-2584800	Weak transcription	HSMM	muscle
22	chr4:2570800-2576200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:2571800-2576200	Enhancers	Brain Anterior Caudate	brain
24	chr4:2571800-2576200	Enhancers	Brain Hippocampus Middle	brain
25	chr4:2571800-2576600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:2572200-2577000	Enhancers	Left Ventricle	heart
27	chr4:2572200-2577000	Enhancers	Right Atrium	heart
28	chr4:2572600-2576200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:2572600-2584000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:2572800-2576200	Weak transcription	Primary B cells from cord blood	blood
31	chr4:2572800-2576400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:2572800-2576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:2572800-2584000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:2573000-2577000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:2573000-2577200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr4:2573000-2577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:2573000-2584000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:2573000-2584000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:2573000-2588400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr4:2573000-2588800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:2573200-2576200	Enhancers	GM12878-XiMat	blood
42	chr4:2573200-2576600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:2573200-2583800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:2573200-2583800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:2573200-2584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:2573200-2585000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:2573200-2585000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr4:2573200-2588600	Weak transcription	Primary T cells from cord blood	blood
49	chr4:2573400-2577200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:2573800-2576200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links