Variant report

Variant	rs1471299
Chromosome Location	chr3:98248863-98248864
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	POLR2A	chr3:98248620-98252823	GM12892	blood:	n/a	n/a
2	BCLAF1	chr3:98248649-98249180	GM12878	blood:	n/a	n/a
3	RUNX3	chr3:98248730-98249155	GM12878	blood:	n/a	n/a
4	RCOR1	chr3:98248795-98249112	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:98248655-98253486	GM15510	blood:	n/a	n/a
6	POLR2A	chr3:98248658-98256543	GM18505	blood:	n/a	n/a
7	POLR2A	chr3:98248710-98249313	GM12878	blood:	n/a	n/a
8	NFIC	chr3:98248541-98249278	GM12878	blood:	n/a	n/a
9	CTCF	chr3:98248820-98248970	GM12872	blood:	n/a	n/a
10	POLR2A	chr3:98248619-98253488	GM12892	blood:	n/a	n/a
11	WRNIP1	chr3:98248753-98249379	GM12878	blood:	n/a	n/a
12	MTA3	chr3:98248591-98249443	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:98248611-98249442	GM12891	blood:	n/a	n/a
14	POU2F2	chr3:98248735-98249198	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:98248683-98253982	GM19099	blood:	n/a	n/a
16	POLR2A	chr3:98248665-98250369	GM12891	blood:	n/a	n/a
17	BHLHE40	chr3:98248762-98249106	GM12878	blood:	n/a	n/a
18	PML	chr3:98245909-98254043	GM12878	blood:	n/a	chr3:98253390-98253398
19	POLR2A	chr3:98248613-98253578	GM12892	blood:	n/a	n/a
20	SPI1	chr3:98248750-98249076	GM12891	blood:	n/a	chr3:98248957-98248970 chr3:98248956-98248969
21	POLR2A	chr3:98248690-98256144	GM19193	blood:	n/a	n/a
22	POLR2A	chr3:98248444-98256619	GM12878	blood:	n/a	n/a
23	NFATC1	chr3:98248840-98253424	GM12878	blood:	n/a	n/a
24	MXI1	chr3:98248781-98249197	GM12878	blood:	n/a	n/a
25	TBP	chr3:98248687-98248989	GM12878	blood:	n/a	n/a
26	EBF1	chr3:98248818-98248982	GM12878	blood:	n/a	n/a
27	PML	chr3:98248723-98249088	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:98248627-98249449	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:98248626-98253505	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:98248630-98254033	GM12878	blood:	n/a	n/a
31	NFATC1	chr3:98248493-98253590	GM12878	blood:	n/a	n/a
32	POU2F2	chr3:98248706-98249322	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:98248622-98252794	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:98248660-98249355	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:98248610-98252751	GM12891	blood:	n/a	n/a
36	POLR2A	chr3:98248703-98256575	GM12892	blood:	n/a	n/a
37	CHD1	chr3:98246186-98256496	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:98248491-98253508	GM12892	blood:	n/a	n/a
39	POLR2A	chr3:98248676-98253986	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
GPR15	TF binding region
RPL38P4	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16839839	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16839882	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16846235	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1961152	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56787128	1.00[EUR][1000 genomes]
rs57985907	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58755405	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58756404	1.00[EUR][1000 genomes]
rs59248577	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60788607	1.00[EUR][1000 genomes]
rs61642998	1.00[EUR][1000 genomes]
rs7626745	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834774	chr3:98108423-98274064	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98242200-98250800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:98245400-98249800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:98246800-98249000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:98246800-98249200	Enhancers	Fetal Intestine Large	intestine
5	chr3:98246800-98249200	Enhancers	Fetal Intestine Small	intestine
6	chr3:98247400-98249200	Enhancers	K562	blood
7	chr3:98248800-98249000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:98248800-98249200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:98248800-98249200	Flanking Active TSS	GM12878-XiMat	blood
10	chr3:98248800-98249400	Active TSS	Rectal Mucosa Donor 29	rectum

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