Variant report

Variant	rs1015022
Chromosome Location	chr21:39878982-39878983
allele	C/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: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11910637	0.95[ASN][1000 genomes]
rs12053740	1.00[YRI][hapmap]
rs2212931	0.92[ASN][1000 genomes]
rs2836443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2836445	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836458	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2836466	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2836469	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2836472	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2836473	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2836474	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs3827204	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7275212	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs9305650	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9636638	1.00[YRI][hapmap]
rs9636936	1.00[YRI][hapmap]

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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:39860400-39879000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:39875000-39879200	Flanking Active TSS	HUVEC	blood vessel
3	chr21:39875200-39879400	Active TSS	Aorta	Aorta
4	chr21:39877000-39879200	Enhancers	NH-A	brain
5	chr21:39877000-39879400	Enhancers	Fetal Heart	heart
6	chr21:39877200-39879000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr21:39877200-39879400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr21:39877200-39880000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:39877400-39879000	Enhancers	Fetal Stomach	stomach
10	chr21:39877400-39879200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr21:39877400-39879200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr21:39877400-39879600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr21:39877600-39879000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:39877600-39879600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr21:39877600-39879800	Weak transcription	Spleen	Spleen
16	chr21:39877600-39880400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr21:39877800-39879000	Enhancers	Fetal Brain Male	brain
18	chr21:39878000-39879200	Enhancers	Primary B cells from cord blood	blood
19	chr21:39878200-39879200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr21:39878200-39879400	Enhancers	Small Intestine	intestine
21	chr21:39878200-39879400	Enhancers	HepG2	liver
22	chr21:39878200-39879600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:39878200-39879600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr21:39878400-39879200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr21:39878400-39879200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr21:39878400-39879400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr21:39878400-39879800	Enhancers	Fetal Muscle Leg	muscle
28	chr21:39878600-39879000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr21:39878600-39879000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr21:39878600-39879000	Active TSS	Primary T cells from cord blood	blood
31	chr21:39878600-39879000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr21:39878600-39879000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr21:39878600-39879000	Active TSS	Adipose Nuclei	Adipose
34	chr21:39878600-39879000	Flanking Active TSS	Fetal Thymus	thymus
35	chr21:39878600-39879000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr21:39878600-39879000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr21:39878600-39879000	Active TSS	Right Atrium	heart
38	chr21:39878600-39879000	Flanking Active TSS	Thymus	Thymus
39	chr21:39878600-39879200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr21:39878600-39879200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr21:39878600-39879200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr21:39878600-39879400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr21:39878600-39879400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr21:39878600-39879400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr21:39878600-39879600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr21:39878600-39879800	Enhancers	Fetal Muscle Trunk	muscle
47	chr21:39878600-39879800	Enhancers	Left Ventricle	heart
48	chr21:39878600-39879800	Enhancers	Lung	lung
49	chr21:39878800-39879000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr21:39878800-39879000	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links