Variant report

Variant	rs60258195
Chromosome Location	chr21:45930228-45930229
allele	C/T
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	chr21:45930130-45930260	GM12891	blood:	n/a	n/a
2	CTCF	chr21:45930089-45931070	SK-N-SH	brain:	n/a	chr21:45930543-45930564 chr21:45930542-45930558 chr21:45930544-45930557 chr21:45930541-45930559 chr21:45930544-45930553 chr21:45930546-45930556 chr21:45930544-45930557
3	MAX	chr21:45930186-45931665	MCF-7	breast:	n/a	chr21:45930955-45930965
4	RAD21	chr21:45930203-45930770	MCF-7	breast:	n/a	chr21:45930543-45930557 chr21:45930547-45930557 chr21:45930547-45930559 chr21:45930542-45930561 chr21:45930379-45930392 chr21:45930545-45930558
5	RAD21	chr21:45930188-45931023	HCT-116	colon:	n/a	chr21:45930543-45930557 chr21:45930547-45930557 chr21:45930547-45930559 chr21:45930542-45930561 chr21:45930379-45930392 chr21:45930545-45930558
6	CTCF	chr21:45930178-45930818	A549	lung:	n/a	chr21:45930543-45930564 chr21:45930542-45930558 chr21:45930544-45930557 chr21:45930541-45930559 chr21:45930544-45930553 chr21:45930546-45930556 chr21:45930544-45930557
7	RAD21	chr21:45930204-45930916	SK-N-SH	brain:	n/a	chr21:45930543-45930557 chr21:45930547-45930557 chr21:45930547-45930559 chr21:45930542-45930561 chr21:45930379-45930392 chr21:45930545-45930558
8	SMC3	chr21:45930219-45930859	SK-N-SH	brain:	n/a	chr21:45930543-45930557 chr21:45930547-45930557
9	STAT3	chr21:45930145-45930345	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr21:45930100-45930250	GM12878	blood:	n/a	n/a
11	CTCF	chr21:45930193-45930268	GM12892	blood:	n/a	n/a
12	CTCF	chr21:45930160-45930310	AG09319	gingival:	n/a	n/a
13	CTCF	chr21:45930203-45930873	HCT-116	colon:	n/a	chr21:45930543-45930564 chr21:45930542-45930558 chr21:45930544-45930557 chr21:45930541-45930559 chr21:45930544-45930553 chr21:45930546-45930556 chr21:45930544-45930557
14	JUN	chr21:45930136-45930840	K562	blood:	n/a	chr21:45930212-45930220 chr21:45930211-45930222 chr21:45930210-45930222
15	CTCF	chr21:45930082-45931009	HCT-116	colon:	n/a	chr21:45930543-45930564 chr21:45930542-45930558 chr21:45930544-45930557 chr21:45930541-45930559 chr21:45930544-45930553 chr21:45930546-45930556 chr21:45930544-45930557
16	CTCF	chr21:45930165-45930991	MCF-7	breast:	n/a	chr21:45930543-45930564 chr21:45930542-45930558 chr21:45930544-45930557 chr21:45930541-45930559 chr21:45930544-45930553 chr21:45930546-45930556 chr21:45930544-45930557
17	CTCF	chr21:45930200-45930350	GM12875	blood:	n/a	n/a
18	RAD21	chr21:45930178-45931031	MCF-7	breast:	n/a	chr21:45930543-45930557 chr21:45930547-45930557 chr21:45930547-45930559 chr21:45930542-45930561 chr21:45930379-45930392 chr21:45930545-45930558

No.	Distal block	Cell Line	Cell type
1	chr21:45928985..45931297-chr21:46219796..46221889,2	MCF-7	breast:
2	chr21:45929071..45931481-chr21:46193501..46196167,2	MCF-7	breast:
3	chr21:45928563..45930238-chr21:46198309..46199884,2	MCF-7	breast:
4	chr21:45927715..45930364-chr21:45931401..45933360,2	MCF-7	breast:
5	chr21:45927714..45931885-chr21:46220128..46224260,6	MCF-7	breast:

Variant related genes	Relation type
TSPEAR-AS1	TF binding region
ENSG00000236519	Chromatin interaction
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17004653	1.00[AFR][1000 genomes]
rs7275583	1.00[AFR][1000 genomes]
rs7284037	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
3	esv3361489	chr21:45669073-46013747	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
4	nsv913918	chr21:45697755-45941566	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv1058359	chr21:45724055-45941566	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
6	nsv1065203	chr21:45731690-45941566	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv544473	chr21:45731690-45941566	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv913942	chr21:45740823-45941566	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv913943	chr21:45740823-46031810	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv1067264	chr21:45757599-45941566	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv544474	chr21:45757599-45941566	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv913944	chr21:45757905-45941566	Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
13	nsv913946	chr21:45838632-46031810	Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv913948	chr21:45860912-46031810	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv1056424	chr21:45894901-46031810	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv544475	chr21:45894901-46031810	Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	nsv1055163	chr21:45895663-46031810	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
18	nsv913949	chr21:45911950-45941566	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45916800-45951600	Weak transcription	Right Atrium	heart
2	chr21:45918000-45930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr21:45925600-45930600	Weak transcription	Primary T cells from cord blood	blood
4	chr21:45926400-45930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:45928200-45930400	Enhancers	Liver	Liver
6	chr21:45928200-45931800	Genic enhancers	HepG2	liver
7	chr21:45928400-45932000	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr21:45928600-45931200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr21:45929000-45930400	Enhancers	Colonic Mucosa	Colon
10	chr21:45929000-45931400	Enhancers	Pancreas	Pancrea
11	chr21:45929400-45930400	Enhancers	HMEC	breast
12	chr21:45929600-45930800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr21:45929600-45931200	Enhancers	Gastric	stomach
14	chr21:45929600-45932000	Genic enhancers	Spleen	Spleen
15	chr21:45929800-45930400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
16	chr21:45929800-45930400	Enhancers	Fetal Intestine Large	intestine
17	chr21:45929800-45930600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:45929800-45930600	Enhancers	Right Ventricle	heart
19	chr21:45929800-45930800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:45929800-45930800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
21	chr21:45929800-45931200	Enhancers	Esophagus	oesophagus
22	chr21:45930000-45930400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr21:45930000-45930400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:45930000-45930600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:45930000-45930800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr21:45930000-45931000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr21:45930000-45931200	Enhancers	Primary B cells from peripheral blood	blood
28	chr21:45930200-45930400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr21:45930200-45930400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr21:45930200-45930400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr21:45930200-45930400	Bivalent Enhancer	Colon Smooth Muscle	Colon
32	chr21:45930200-45930400	Enhancers	Fetal Brain Male	brain
33	chr21:45930200-45930400	Enhancers	Fetal Intestine Small	intestine
34	chr21:45930200-45930600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr21:45930200-45930600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr21:45930200-45930600	Enhancers	Primary hematopoietic stem cells	blood
37	chr21:45930200-45930600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr21:45930200-45930600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr21:45930200-45930600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr21:45930200-45930600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr21:45930200-45930600	Bivalent Enhancer	Placenta	Placenta
42	chr21:45930200-45930600	Enhancers	Left Ventricle	heart
43	chr21:45930200-45930600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
44	chr21:45930200-45930600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
45	chr21:45930200-45930800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr21:45930200-45930800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
47	chr21:45930200-45930800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr21:45930200-45930800	Enhancers	Stomach Mucosa	stomach
49	chr21:45930200-45931000	Enhancers	Primary B cells from cord blood	blood
50	chr21:45930200-45931000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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