Variant report

Variant	rs1561253
Chromosome Location	chr2:86832394-86832395
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	chr2:86832166..86835241-chr2:86849689..86852205,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239305	Chromatin interaction
ENSG00000249884	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10496321	1.00[MEX][hapmap]
rs10520428	0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2044233	1.00[AMR][1000 genomes]
rs2044234	1.00[MEX][hapmap]
rs4341929	1.00[AMR][1000 genomes]
rs56863297	0.87[AMR][1000 genomes]
rs57124922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61248967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72934428	1.00[AMR][1000 genomes]
rs73949837	0.98[AFR][1000 genomes];1.00[AMR][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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
2	chr2:86824600-86840600	Weak transcription	Fetal Heart	heart
3	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:86826800-86842000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:86826800-86847800	Weak transcription	NHEK	skin
6	chr2:86827200-86835600	Weak transcription	Brain Germinal Matrix	brain
7	chr2:86828200-86847800	Weak transcription	NHLF	lung
8	chr2:86828800-86836000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:86829000-86833000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:86829000-86845400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:86829200-86833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:86829200-86833200	Strong transcription	Ovary	ovary
13	chr2:86829200-86833200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:86829200-86835800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:86829400-86835400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:86829400-86835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:86829400-86848400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:86829400-86849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:86829600-86835200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:86829600-86836000	Weak transcription	Spleen	Spleen
21	chr2:86829600-86846200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:86829800-86846000	Weak transcription	NH-A	brain
23	chr2:86829800-86849400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:86830000-86832800	Strong transcription	Primary B cells from cord blood	blood
25	chr2:86830000-86833200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:86830000-86839400	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:86830000-86846200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:86830000-86848600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:86830200-86833600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:86830400-86846200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:86830400-86847600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:86830400-86848600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:86830600-86834200	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:86830600-86839600	Strong transcription	Adipose Nuclei	Adipose
35	chr2:86830600-86847000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:86830800-86832600	Strong transcription	Primary T cells from cord blood	blood
37	chr2:86830800-86832600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr2:86830800-86832600	Strong transcription	Colon Smooth Muscle	Colon
39	chr2:86830800-86832600	Strong transcription	A549	lung
40	chr2:86830800-86832800	Strong transcription	Fetal Lung	lung
41	chr2:86830800-86833200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:86830800-86833200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:86830800-86833200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:86830800-86833200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:86830800-86835000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:86830800-86836000	Strong transcription	Osteobl	bone
47	chr2:86830800-86836400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:86830800-86845000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:86830800-86845600	Strong transcription	Dnd41	blood
50	chr2:86830800-86847600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links