Variant report

Variant	rs2008644
Chromosome Location	chr10:52020424-52020425
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	SPI1	chr10:52020399-52020838	GM12891	blood:	n/a	chr10:52020609-52020622 chr10:52020608-52020621
2	NFIC	chr10:52020329-52021091	GM12878	blood:	n/a	n/a
3	EP300	chr10:52020363-52020987	GM12878	blood:	n/a	chr10:52020683-52020697 chr10:52020611-52020620
4	CREB1	chr10:52020370-52020962	GM12878	blood:	n/a	n/a
5	MEF2A	chr10:52020407-52020932	K562	blood:	n/a	chr10:52020671-52020686 chr10:52020673-52020682 chr10:52020670-52020686 chr10:52020666-52020687 chr10:52020672-52020683 chr10:52020666-52020687 chr10:52020670-52020685 chr10:52020671-52020685 chr10:52020670-52020685 chr10:52020666-52020687
6	EP300	chr10:52020364-52020984	GM12878	blood:	n/a	chr10:52020683-52020697 chr10:52020611-52020620
7	NFYB	chr10:52020251-52020860	GM12878	blood:	n/a	n/a
8	MEF2C	chr10:52020322-52021037	GM12878	blood:	n/a	chr10:52020669-52020684 chr10:52020671-52020686 chr10:52020673-52020682 chr10:52020670-52020686 chr10:52020666-52020687 chr10:52020672-52020683 chr10:52020666-52020687 chr10:52020353-52020368 chr10:52020670-52020685 chr10:52020671-52020685 chr10:52020666-52020687
9	CREB1	chr10:52020424-52020883	GM12878	blood:	n/a	n/a
10	RCOR1	chr10:52020418-52021091	GM12878	blood:	n/a	n/a
11	IRF1	chr10:52019954-52020963	K562	blood:	n/a	chr10:52020308-52020322 chr10:52020681-52020695 chr10:52020680-52020694 chr10:52020680-52020691 chr10:52020684-52020698 chr10:52020682-52020692 chr10:52020681-52020694 chr10:52020682-52020696 chr10:52020681-52020694 chr10:52020680-52020700
12	NFATC1	chr10:52020377-52021012	GM12878	blood:	n/a	n/a
13	TEAD4	chr10:52020410-52020931	K562	blood:	n/a	n/a
14	RUNX3	chr10:52020368-52021017	GM12878	blood:	n/a	n/a
15	ZNF384	chr10:52020346-52021002	GM12878	blood:	n/a	n/a
16	SPI1	chr10:52020380-52020874	HL-60	blood:	n/a	chr10:52020609-52020622 chr10:52020608-52020621
17	SPI1	chr10:52020251-52021198	GM12878	blood:	n/a	chr10:52020609-52020622 chr10:52020608-52020621
18	MTA3	chr10:52020397-52020991	GM12878	blood:	n/a	n/a
19	MEF2A	chr10:52020275-52021021	GM12878	blood:	n/a	chr10:52020671-52020686 chr10:52020673-52020682 chr10:52020670-52020686 chr10:52020666-52020687 chr10:52020672-52020683 chr10:52020666-52020687 chr10:52020353-52020368 chr10:52020670-52020685 chr10:52020671-52020685 chr10:52020670-52020685 chr10:52020666-52020687
20	TBL1XR1	chr10:52020424-52021138	GM12878	blood:	n/a	n/a
21	ATF2	chr10:52020317-52021056	GM12878	blood:	n/a	n/a
22	BHLHE40	chr10:52020017-52021035	GM12878	blood:	n/a	n/a
23	MEF2A	chr10:52020373-52021018	GM12878	blood:	n/a	chr10:52020671-52020686 chr10:52020673-52020682 chr10:52020670-52020686 chr10:52020666-52020687 chr10:52020672-52020683 chr10:52020666-52020687 chr10:52020670-52020685 chr10:52020671-52020685 chr10:52020670-52020685 chr10:52020666-52020687
24	SPI1	chr10:52020400-52020807	GM12878	blood:	n/a	chr10:52020609-52020622 chr10:52020608-52020621
25	CUX1	chr10:52020373-52021155	GM12878	blood:	n/a	n/a
26	MXI1	chr10:52020374-52020971	GM12878	blood:	n/a	n/a
27	FOXM1	chr10:52020396-52020977	GM12878	blood:	n/a	n/a
28	NFIC	chr10:52020249-52021069	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
DYNC1I2P1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1369863	0.90[EUR][1000 genomes]
rs1369864	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1865747	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs1865748	0.90[EUR][1000 genomes]
rs2043614	0.90[EUR][1000 genomes]
rs2043615	0.90[EUR][1000 genomes]
rs2043617	0.90[EUR][1000 genomes]
rs2043618	0.90[EUR][1000 genomes]
rs2060562	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2196463	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2217900	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2574948	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574949	0.92[ASN][1000 genomes]
rs2574984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813298	0.96[EUR][1000 genomes]
rs2813300	0.80[EUR][1000 genomes]
rs2813301	0.90[EUR][1000 genomes]
rs2813306	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2813307	0.90[EUR][1000 genomes]
rs2813309	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1053293	chr10:51981959-52102649	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2008644	ZNF488	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52019400-52022200	Enhancers	Fetal Intestine Small	intestine
2	chr10:52019400-52022400	Enhancers	K562	blood
3	chr10:52019400-52022600	Enhancers	Fetal Intestine Large	intestine
4	chr10:52019800-52020800	Weak transcription	Small Intestine	intestine
5	chr10:52020000-52023000	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:52020200-52020600	Enhancers	Duodenum Mucosa	Duodenum
7	chr10:52020200-52021400	Enhancers	Primary hematopoietic stem cells	blood
8	chr10:52020200-52021400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:52020200-52021400	Flanking Active TSS	GM12878-XiMat	blood
10	chr10:52020200-52021600	Enhancers	Primary B cells from cord blood	blood
11	chr10:52020400-52020600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:52020400-52022200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links