Variant report

Variant	rs58940818
Chromosome Location	chr21:45664784-45664785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr21:45663053-45664958	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:45652131-45665869	GM12878	blood:	n/a	n/a
3	MTA3	chr21:45664674-45666548	GM12878	blood:	n/a	n/a
4	POLR2A	chr21:45658587-45668327	PFSK-1	brain:	n/a	n/a
5	NFIC	chr21:45664762-45666529	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:45657802-45669043	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr21:45660624-45668864	GM12891	blood:	n/a	n/a
8	MTA3	chr21:45660829-45666640	GM12878	blood:	n/a	n/a
9	PML	chr21:45660477-45666388	GM12878	blood:	n/a	chr21:45664300-45664308 chr21:45665810-45665818

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45662131..45665488-chr21:45759079..45762763,3	MCF-7	breast:
2	chr21:45622629..45624491-chr21:45663848..45665509,2	MCF-7	breast:
3	chr21:45664753..45666308-chr21:45706084..45707885,2	MCF-7	breast:
4	chr21:45664074..45664939-chr21:45687442..45688212,2	MCF-7	breast:
5	chr21:45603147..45604698-chr21:45662988..45665089,2	MCF-7	breast:
6	chr21:45588410..45594838-chr21:45658945..45665595,14	MCF-7	breast:
7	chr21:45554484..45558321-chr21:45662336..45665430,3	MCF-7	breast:
8	chr21:45658211..45662255-chr21:45662719..45665336,3	K562	blood:
9	chr21:45620311..45631567-chr21:45651002..45670824,52	MCF-7	breast:
10	chr21:45658941..45665769-chr21:45718013..45724632,19	MCF-7	breast:
11	chr21:45663828..45666335-chr21:45687884..45690743,2	MCF-7	breast:
12	chr21:45658347..45670658-chr21:45718073..45723358,28	MCF-7	breast:

No data

Variant related genes	Relation type
ICOSLG	TF binding region
ENSG00000141959	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000267913	Chromatin interaction
ENSG00000160221	Chromatin interaction
ENSG00000160226	Chromatin interaction
ENSG00000232124	Chromatin interaction
ENSG00000232969	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2838514	1.00[ASN][1000 genomes]
rs2838523	1.00[ASN][1000 genomes]
rs378993	1.00[ASN][1000 genomes]
rs41277544	1.00[ASN][1000 genomes]
rs41277552	1.00[ASN][1000 genomes]
rs45566431	1.00[ASN][1000 genomes]
rs59738122	1.00[ASN][1000 genomes]
rs59829171	1.00[ASN][1000 genomes]
rs62220372	1.00[ASN][1000 genomes]
rs62220373	1.00[ASN][1000 genomes]
rs62220410	1.00[ASN][1000 genomes]
rs6518349	1.00[ASN][1000 genomes]
rs7276055	1.00[ASN][1000 genomes]
rs7277916	1.00[ASN][1000 genomes]
rs73381309	1.00[ASN][1000 genomes]
rs73381322	1.00[ASN][1000 genomes]
rs73381331	1.00[ASN][1000 genomes]
rs8126899	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
9	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
10	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
11	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv459295	chr21:45629565-45849864	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
14	nsv587740	chr21:45629565-45849864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	57 gene(s)	inside rSNPs	diseases
15	nsv913904	chr21:45636881-45700641	Genic enhancers Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv913905	chr21:45640629-45696025	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv913906	chr21:45657970-45818609	Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45661800-45668200	Enhancers	Liver	Liver
2	chr21:45662000-45665000	Enhancers	Stomach Mucosa	stomach
3	chr21:45662400-45664800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr21:45662400-45665400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr21:45662800-45667800	Weak transcription	Brain Anterior Caudate	brain
6	chr21:45662800-45705600	Weak transcription	Right Atrium	heart
7	chr21:45663200-45665800	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr21:45663200-45666000	Flanking Active TSS	GM12878-XiMat	blood
9	chr21:45663400-45666200	Enhancers	Primary hematopoietic stem cells	blood
10	chr21:45663600-45665000	Enhancers	Fetal Intestine Small	intestine
11	chr21:45663600-45670400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr21:45663800-45664800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr21:45663800-45665000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr21:45663800-45668400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr21:45663800-45668400	Enhancers	HepG2	liver
16	chr21:45663800-45669600	Enhancers	Fetal Intestine Large	intestine
17	chr21:45664000-45665400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr21:45664000-45665600	Enhancers	Primary T cells from cord blood	blood
19	chr21:45664000-45665800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr21:45664000-45665800	Enhancers	Spleen	Spleen
21	chr21:45664000-45666200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr21:45664000-45667800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:45664000-45671800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:45664200-45665200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr21:45664200-45665200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr21:45664200-45667000	Weak transcription	Esophagus	oesophagus
27	chr21:45664400-45664800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
28	chr21:45664400-45665200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr21:45664400-45665600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr21:45664400-45665600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr21:45664400-45665800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr21:45664400-45666000	Enhancers	Fetal Thymus	thymus
33	chr21:45664400-45667200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr21:45664400-45668200	Weak transcription	Gastric	stomach
35	chr21:45664400-45668400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr21:45664600-45665000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr21:45664600-45665000	Weak transcription	HSMMtube	muscle
38	chr21:45664600-45665600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr21:45664600-45667000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr21:45664600-45667200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr21:45664600-45667600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr21:45664600-45668000	Weak transcription	Hela-S3	cervix
43	chr21:45664600-45669400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr21:45664600-45669800	Enhancers	Primary B cells from peripheral blood	blood

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