Variant report

Variant	rs58899027
Chromosome Location	chr4:143465318-143465319
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143390493..143399629-chr4:143464669..143473703,24	MCF-7	breast:
2	chr4:143463931..143465579-chr4:143468036..143470044,2	MCF-7	breast:
3	chr4:143392027..143397179-chr4:143464314..143467113,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10013367	0.81[ASN][1000 genomes]
rs10519649	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11100748	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100749	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11100750	0.81[ASN][1000 genomes]
rs1160379	0.85[ASN][1000 genomes]
rs11930912	0.87[EUR][1000 genomes]
rs11939291	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11943687	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12504375	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12504378	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12504770	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1425518	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1425519	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1476122	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1559709	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16998558	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17016344	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17016354	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17016379	0.83[ASN][1000 genomes]
rs17717651	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1963849	0.83[ASN][1000 genomes]
rs1974940	0.81[ASN][1000 genomes]
rs2059510	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2059511	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2059513	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2217016	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34007357	0.85[ASN][1000 genomes]
rs34223306	0.81[ASN][1000 genomes]
rs35854467	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4246729	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4524461	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975306	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975312	0.82[ASN][1000 genomes]
rs4975313	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975314	0.81[ASN][1000 genomes]
rs4975316	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975317	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975318	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57201046	0.83[ASN][1000 genomes]
rs57260347	0.83[ASN][1000 genomes]
rs58078405	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59732892	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60951295	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61104737	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61142249	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537109	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6537110	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67078907	0.81[ASN][1000 genomes]
rs67311549	0.83[ASN][1000 genomes]
rs67900719	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6814775	0.83[ASN][1000 genomes]
rs6816875	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6826090	0.81[ASN][1000 genomes]
rs7655599	0.81[ASN][1000 genomes]
rs7671198	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890191	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs890192	0.88[ASN][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	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	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143444800-143468400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:143456800-143468400	Weak transcription	HMEC	breast
3	chr4:143457000-143466600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:143461400-143471000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:143461800-143466200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:143463000-143472200	Weak transcription	Aorta	Aorta
7	chr4:143463200-143465400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:143463200-143470200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:143463400-143465400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:143463400-143468600	Weak transcription	Left Ventricle	heart
11	chr4:143464000-143466600	Enhancers	Fetal Intestine Small	intestine
12	chr4:143464400-143466000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr4:143465000-143465600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:143465000-143466000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:143465000-143466800	Enhancers	Fetal Intestine Large	intestine
16	chr4:143465200-143465600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr4:143465200-143465600	Enhancers	Fetal Lung	lung
18	chr4:143465200-143466000	Enhancers	Dnd41	blood
19	chr4:143465200-143470600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links