Variant report

Variant	rs58423878
Chromosome Location	chr2:39645910-39645911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39643804..39646063-chr2:39663666..39665517,2	MCF-7	breast:
2	chr2:39643207..39646078-chr2:39648407..39650074,2	K562	blood:
3	chr2:39643905..39646272-chr2:39657496..39659810,2	MCF-7	breast:
4	chr2:39642094..39644271-chr2:39644504..39647283,3	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs59367765	0.84[AFR][1000 genomes]
rs72929170	1.00[AMR][1000 genomes]
rs72929174	1.00[AMR][1000 genomes]
rs72929178	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931126	1.00[AMR][1000 genomes]
rs72931142	1.00[AMR][1000 genomes]
rs72931146	1.00[AMR][1000 genomes]
rs7603259	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39636600-39651400	Weak transcription	Fetal Thymus	thymus
2	chr2:39637200-39647000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:39637600-39651400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:39638800-39652400	Weak transcription	Hela-S3	cervix
6	chr2:39639000-39649000	Weak transcription	Primary T cells from cord blood	blood
7	chr2:39639200-39658000	Weak transcription	Fetal Stomach	stomach
8	chr2:39639600-39646800	Weak transcription	Fetal Lung	lung
9	chr2:39639600-39657200	Weak transcription	HMEC	breast
10	chr2:39640600-39647600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:39640800-39647000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:39640800-39647000	Weak transcription	Spleen	Spleen
13	chr2:39640800-39649200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:39640800-39652400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:39640800-39656800	Weak transcription	NH-A	brain
16	chr2:39640800-39660000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:39641000-39646600	Weak transcription	Aorta	Aorta
18	chr2:39641000-39651600	Weak transcription	HSMMtube	muscle
19	chr2:39641000-39656600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:39641200-39646000	Weak transcription	HSMM	muscle
21	chr2:39641200-39650200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:39641200-39659600	Weak transcription	Brain Angular Gyrus	brain
23	chr2:39641400-39649200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:39642400-39646000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:39642400-39647400	Enhancers	Rectal Smooth Muscle	rectum
26	chr2:39643200-39647200	Enhancers	Fetal Heart	heart
27	chr2:39643200-39647400	Enhancers	A549	lung
28	chr2:39643400-39646200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:39643400-39646400	Enhancers	Adipose Nuclei	Adipose
30	chr2:39643400-39646800	Enhancers	Osteobl	bone
31	chr2:39643400-39647400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr2:39643400-39647400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr2:39643600-39646400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:39643600-39646800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:39643800-39646000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:39643800-39646200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:39643800-39647000	Weak transcription	Brain Germinal Matrix	brain
38	chr2:39644200-39646200	Enhancers	Liver	Liver
39	chr2:39644200-39646600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:39644200-39646800	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:39644200-39650000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:39644400-39646200	Enhancers	Stomach Mucosa	stomach
44	chr2:39644400-39654200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:39644400-39654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:39644800-39646400	Enhancers	Ovary	ovary
47	chr2:39644800-39646400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:39644800-39647200	Enhancers	K562	blood
49	chr2:39644800-39650600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:39645000-39646200	Enhancers	Gastric	stomach

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