Variant report

Variant	rs28410139
Chromosome Location	chr4:82389433-82389434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:82388377..82389917-chr4:82765729..82766486,4	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10018892	0.83[AMR][1000 genomes]
rs10019254	0.83[AMR][1000 genomes]
rs10440362	0.85[EUR][1000 genomes]
rs13353696	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28393966	0.83[AMR][1000 genomes]
rs28408727	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56934019	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6846142	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72884907	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73829600	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7693787	0.91[AMR][1000 genomes];0.92[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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS 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	7 gene(s)	inside rSNPs	diseases
3	nsv829986	chr4:82345163-82509860	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82352400-82390000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:82354200-82390800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:82362200-82389800	Weak transcription	Fetal Brain Male	brain
4	chr4:82363600-82390400	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:82363600-82391000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:82368200-82391400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:82369400-82390000	Weak transcription	Brain Germinal Matrix	brain
8	chr4:82369600-82391000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:82373600-82390000	Weak transcription	Thymus	Thymus
10	chr4:82377800-82390800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:82377800-82391000	Weak transcription	Dnd41	blood
12	chr4:82378200-82390000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:82378600-82390800	Weak transcription	Fetal Stomach	stomach
14	chr4:82379000-82391400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:82380600-82391000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:82380600-82391200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:82380600-82391200	Weak transcription	Placenta	Placenta
18	chr4:82381600-82390400	Weak transcription	Fetal Thymus	thymus
19	chr4:82381800-82390400	Weak transcription	Esophagus	oesophagus
20	chr4:82382000-82390400	Weak transcription	Lung	lung
21	chr4:82383200-82390000	Weak transcription	Adipose Nuclei	Adipose
22	chr4:82383200-82390400	Weak transcription	Gastric	stomach
23	chr4:82383200-82391000	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:82383600-82390200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:82384000-82389800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:82384000-82390000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:82385400-82390000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:82385400-82390000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:82387000-82389800	Weak transcription	Small Intestine	intestine
30	chr4:82387000-82391000	Weak transcription	Colonic Mucosa	Colon
31	chr4:82387000-82391400	Weak transcription	Psoas Muscle	Psoas
32	chr4:82387400-82391000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:82387600-82390400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:82387600-82391000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:82388200-82390800	Enhancers	Primary T cells from cord blood	blood
36	chr4:82388400-82389800	Enhancers	Primary B cells from cord blood	blood
37	chr4:82388400-82390200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:82388400-82391000	Enhancers	Primary B cells from peripheral blood	blood
39	chr4:82388400-82391000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:82388600-82390000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:82388600-82390000	Weak transcription	Stomach Mucosa	stomach
42	chr4:82388600-82390200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:82388600-82391400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:82388800-82389800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr4:82388800-82390000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr4:82388800-82391200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr4:82388800-82391600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:82389000-82389600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:82389000-82389800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:82389000-82389800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links