Variant report

Variant	rs2836452
Chromosome Location	chr21:39879350-39879351
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	chr21:39868178..39870338-chr21:39876801..39879710,3	MCF-7	breast:
2	chr21:39876376..39879453-chr21:40175999..40179408,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2836437	0.87[CEU][hapmap]
rs2836447	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836478	0.81[MEX][hapmap]
rs3787907	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7277942	0.93[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs73906314	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059340	chr21:39817504-39881353	Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:39875200-39879400	Active TSS	Aorta	Aorta
2	chr21:39877000-39879400	Enhancers	Fetal Heart	heart
3	chr21:39877200-39879400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:39877200-39880000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr21:39877400-39879600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr21:39877600-39879600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr21:39877600-39879800	Weak transcription	Spleen	Spleen
8	chr21:39877600-39880400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr21:39878200-39879400	Enhancers	Small Intestine	intestine
10	chr21:39878200-39879400	Enhancers	HepG2	liver
11	chr21:39878200-39879600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:39878200-39879600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr21:39878400-39879400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr21:39878400-39879800	Enhancers	Fetal Muscle Leg	muscle
15	chr21:39878600-39879400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr21:39878600-39879400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr21:39878600-39879400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr21:39878600-39879600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr21:39878600-39879800	Enhancers	Fetal Muscle Trunk	muscle
20	chr21:39878600-39879800	Enhancers	Left Ventricle	heart
21	chr21:39878600-39879800	Enhancers	Lung	lung
22	chr21:39878800-39879800	Enhancers	Placenta	Placenta
23	chr21:39878800-39880000	Enhancers	Fetal Lung	lung
24	chr21:39879000-39879400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr21:39879000-39879400	Enhancers	Thymus	Thymus
26	chr21:39879000-39879600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr21:39879000-39879600	Enhancers	Primary hematopoietic stem cells	blood
28	chr21:39879000-39879600	Bivalent Enhancer	Fetal Stomach	stomach
29	chr21:39879000-39879600	Enhancers	Fetal Thymus	thymus
30	chr21:39879000-39879600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr21:39879000-39879600	Enhancers	Right Atrium	heart
32	chr21:39879000-39879600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
33	chr21:39879000-39879800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr21:39879000-39879800	Enhancers	Duodenum Mucosa	Duodenum
35	chr21:39879200-39879400	Bivalent Enhancer	Brain Hippocampus Middle	brain
36	chr21:39879200-39879600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:39879200-39879600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr21:39879200-39879600	Enhancers	Primary T cells from cord blood	blood
39	chr21:39879200-39879600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr21:39879200-39879800	Weak transcription	Right Ventricle	heart
41	chr21:39879200-39879800	Enhancers	HUVEC	blood vessel
42	chr21:39879200-39879800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr21:39879200-39880400	Weak transcription	Colonic Mucosa	Colon
44	chr21:39879200-39882000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr21:39879200-39882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links