Variant report

Variant	rs2892829
Chromosome Location	chr4:119773119-119773120
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	chr4:119758473..119760374-chr4:119771765..119773281,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNPO2-1	chr4:119771440-119773194	NONHSAT098023

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10471012	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857061	0.94[ASN][1000 genomes]
rs1365548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1896185	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2017575	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389687	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2389691	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4240322	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4834708	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6830196	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6838071	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6843524	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7676892	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3376985	chr4:119757182-119774736	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS 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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119771000-119773400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:119771200-119773400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr4:119771200-119773600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr4:119771400-119773400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr4:119771600-119773800	Active TSS	GM12878-XiMat	blood
6	chr4:119771800-119773600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:119772000-119773200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:119772200-119774400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:119772400-119773400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:119772400-119773400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:119772400-119773400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:119772400-119773400	Enhancers	Liver	Liver
13	chr4:119772400-119774000	Weak transcription	HUVEC	blood vessel
14	chr4:119772400-119779200	Weak transcription	Ovary	ovary
15	chr4:119772400-119788200	Weak transcription	NHDF-Ad	bronchial
16	chr4:119772600-119773200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:119772600-119773200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:119772600-119773200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr4:119772600-119773200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr4:119772600-119773600	Enhancers	Primary B cells from cord blood	blood
21	chr4:119772800-119773200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:119772800-119773200	Enhancers	Dnd41	blood
23	chr4:119772800-119773400	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr4:119773000-119773200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:119773000-119773400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:119773000-119773400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr4:119773000-119773600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr4:119773000-119775000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links