Variant report

Variant	rs28382590
Chromosome Location	chr6:28493585-28493586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:28493580-28493730	HEK293	kidney:	n/a	n/a
2	NR2F2	chr6:28493435-28493731	K562	blood:	n/a	n/a
3	NR2F2	chr6:28493326-28493856	K562	blood:	n/a	n/a
4	MYC	chr6:28493473-28493857	K562	blood:	n/a	n/a
5	RCOR1	chr6:28493437-28493713	K562	blood:	n/a	n/a
6	EGR1	chr6:28493445-28493755	K562	blood:	n/a	n/a
7	EP300	chr6:28493459-28493730	K562	blood:	n/a	n/a
8	TEAD4	chr6:28493300-28493868	K562	blood:	n/a	n/a
9	JUND	chr6:28493397-28493799	K562	blood:	n/a	n/a
10	MAX	chr6:28493489-28493768	NB4	blood:	n/a	n/a
11	TRIM28	chr6:28493385-28493721	K562	blood:	n/a	n/a
12	BHLHE40	chr6:28493523-28493729	K562	blood:	n/a	n/a
13	MAX	chr6:28493459-28493719	K562	blood:	n/a	n/a
14	MAZ	chr6:28493467-28493755	K562	blood:	n/a	n/a
15	MYC	chr6:28493523-28493812	NB4	blood:	n/a	n/a
16	ZBTB7A	chr6:28493490-28493784	K562	blood:	n/a	n/a
17	GABPA	chr6:28493394-28493759	K562	blood:	n/a	n/a
18	CTCF	chr6:28493580-28493730	K562	blood:	n/a	n/a
19	MAX	chr6:28493421-28493852	K562	blood:	n/a	chr6:28493452-28493461

Variant related genes	Relation type
GPX5	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2079705	1.00[CEU][hapmap]
rs2232430	0.87[CEU][hapmap]
rs2394101	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs28382595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382602	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382603	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382609	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382614	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28745594	1.00[EUR][1000 genomes]
rs34757087	1.00[EUR][1000 genomes]
rs34951544	1.00[EUR][1000 genomes]
rs35062161	1.00[EUR][1000 genomes]
rs35758328	1.00[EUR][1000 genomes]
rs41270579	0.84[EUR][1000 genomes]
rs41270593	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270596	0.90[EUR][1000 genomes]
rs4412194	0.87[CEU][hapmap]
rs4540253	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs55920503	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965649	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043329	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975420	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58078500	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59653352	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844212	0.84[EUR][1000 genomes]
rs72844223	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844224	0.86[EUR][1000 genomes]
rs72844225	0.86[EUR][1000 genomes]
rs72844226	0.86[EUR][1000 genomes]
rs72844244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850077	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850094	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854542	0.84[EUR][1000 genomes]
rs72854546	0.84[EUR][1000 genomes]
rs72854553	0.84[EUR][1000 genomes]
rs72854556	0.84[EUR][1000 genomes]
rs7770236	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468379	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 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	chr6:28490000-28493600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr6:28492800-28493600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr6:28493000-28493600	Enhancers	Primary T cells fromperipheralblood	blood
4	chr6:28493000-28494000	Bivalent Enhancer	Primary T cells from cord blood	blood
5	chr6:28493000-28494000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:28493000-28494000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:28493000-28494000	Bivalent Enhancer	Dnd41	blood
8	chr6:28493000-28494600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:28493200-28493800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr6:28493200-28494200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:28493200-28494200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:28493400-28493600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:28493400-28493600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:28493400-28493800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:28493400-28493800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:28493400-28493800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:28493400-28493800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:28493400-28493800	Bivalent Enhancer	Fetal Thymus	thymus
19	chr6:28493400-28494000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:28493400-28494000	Flanking Active TSS	K562	blood

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