Variant report

Variant	rs61041466
Chromosome Location	chr4:99180366-99180367
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:99180313-99182895	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr4:99180251-99183139	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:99063087..99065504-chr4:99179455..99182247,2	MCF-7	breast:
2	chr4:99180005..99182414-chr4:99204613..99206874,2	K562	blood:
3	chr4:99166826..99169265-chr4:99180288..99182314,2	MCF-7	breast:
4	chr4:99062262..99068404-chr4:99178848..99183768,9	MCF-7	breast:
5	chr20:55837025..55838965-chr4:99178641..99181460,2	MCF-7	breast:
6	chr4:99177008..99180462-chr4:99180782..99182422,3	K562	blood:
7	chr4:99076051..99077551-chr4:99180191..99182364,2	MCF-7	breast:

No data

Variant related genes	Relation type
RAP1GDS1	TF binding region
ENSG00000163116	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28651913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2866008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683554	1.00[EUR][1000 genomes]
rs58408865	1.00[EUR][1000 genomes]
rs58485619	1.00[EUR][1000 genomes]
rs58977062	1.00[EUR][1000 genomes]
rs59516498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59929475	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60266816	1.00[EUR][1000 genomes]
rs60470511	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72883608	1.00[EUR][1000 genomes]
rs72883610	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72883612	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72883618	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892332	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892346	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892347	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892354	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892355	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892368	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892376	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72894293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72894299	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72894392	1.00[EUR][1000 genomes]
rs72896117	1.00[EUR][1000 genomes]
rs72896309	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72896311	1.00[EUR][1000 genomes]
rs72896316	1.00[EUR][1000 genomes]
rs72896319	1.00[EUR][1000 genomes]
rs72896324	1.00[EUR][1000 genomes]
rs72896325	1.00[EUR][1000 genomes]
rs72896335	1.00[EUR][1000 genomes]
rs72896338	1.00[EUR][1000 genomes]
rs72896342	1.00[EUR][1000 genomes]
rs72896346	1.00[EUR][1000 genomes]
rs72896356	1.00[EUR][1000 genomes]
rs72896358	1.00[EUR][1000 genomes]
rs72896365	1.00[EUR][1000 genomes]
rs72896389	1.00[EUR][1000 genomes]
rs72898341	1.00[EUR][1000 genomes]
rs72898343	1.00[EUR][1000 genomes]
rs72898363	1.00[EUR][1000 genomes]
rs72898376	1.00[EUR][1000 genomes]
rs72898388	1.00[EUR][1000 genomes]
rs72898393	1.00[EUR][1000 genomes]
rs72900361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900365	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900388	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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	13 gene(s)	inside rSNPs	diseases
10	esv3429055	chr4:99180179-99180462	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99164400-99180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:99171600-99181000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:99174800-99180800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:99175000-99180400	Weak transcription	Liver	Liver
5	chr4:99175600-99180600	Weak transcription	HepG2	liver
6	chr4:99175800-99180600	Weak transcription	Brain Anterior Caudate	brain
7	chr4:99176600-99180600	Weak transcription	Fetal Brain Male	brain
8	chr4:99178400-99180600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:99179600-99180600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:99179600-99180600	Enhancers	Dnd41	blood
11	chr4:99179800-99180600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:99179800-99180600	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:99179800-99180600	Enhancers	Fetal Heart	heart
14	chr4:99180000-99180400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:99180000-99180400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:99180200-99181000	Enhancers	Fetal Muscle Trunk	muscle

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