Variant report

Variant	rs12644565
Chromosome Location	chr4:143368049-143368050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143366881..143368916-chr4:143406603..143409121,2	MCF-7	breast:
2	chr4:143367680..143375723-chr4:143391908..143397720,10	MCF-7	breast:
3	chr4:143363779..143366801-chr4:143367868..143370229,3	K562	blood:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10012476	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015184	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015271	0.90[EUR][1000 genomes]
rs1013397	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642500	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12643136	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs12646243	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12649139	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1364917	0.85[CEU][hapmap]
rs1364918	0.85[CEU][hapmap]
rs1364919	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs1364920	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs1364926	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1425534	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1425535	0.85[CEU][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1425538	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1603584	0.85[ASN][1000 genomes]
rs17016170	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17016195	0.89[EUR][1000 genomes]
rs17016207	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17016248	0.85[CEU][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17016284	0.83[AMR][1000 genomes]
rs17016304	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs2042644	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2113997	0.82[ASN][1000 genomes]
rs2162108	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2322705	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322706	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2322796	0.83[AMR][1000 genomes]
rs28510314	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28823374	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28850298	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28861843	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34900920	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3913164	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3913165	0.89[EUR][1000 genomes]
rs4345256	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57724540	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59784151	0.84[AMR][1000 genomes]
rs60004938	0.80[AMR][1000 genomes]
rs6822263	1.00[CEU][hapmap]
rs6823362	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7662794	0.89[EUR][1000 genomes]
rs7668133	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7672965	0.92[ASN][1000 genomes]
rs7695918	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7699408	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9308152	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931637	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs979511	1.00[CEU][hapmap]
rs9986090	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998089	0.85[AMR][1000 genomes];0.89[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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143351200-143371200	Weak transcription	Pancreas	Pancrea
2	chr4:143357400-143371200	Weak transcription	Aorta	Aorta
3	chr4:143366200-143369200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr4:143367000-143371000	Weak transcription	Psoas Muscle	Psoas
5	chr4:143367000-143392600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:143367400-143369400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:143367600-143368200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:143367800-143368200	Enhancers	HSMMtube	muscle
9	chr4:143367800-143368400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr4:143367800-143368600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr4:143367800-143368600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:143367800-143368600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:143367800-143368800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:143367800-143369400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:143367800-143369400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr4:143368000-143368200	Enhancers	Fetal Heart	heart
17	chr4:143368000-143368400	Active TSS	Primary hematopoietic stem cells	blood
18	chr4:143368000-143368400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr4:143368000-143368600	Enhancers	Primary T cells from cord blood	blood
20	chr4:143368000-143369000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links