Variant report

Variant	rs2488457
Chromosome Location	chr1:114415368-114415369
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:114415210-114415393	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr1:114414088-114415420	GM12878	blood:	n/a	n/a
3	STAT3	chr1:114415157-114415601	MCF10A-Er-Src	breast:	n/a	chr1:114415529-114415536
4	FOS	chr1:114415304-114415386	MCF10A-Er-Src	breast:	n/a	n/a
5	SPI1	chr1:114414639-114415706	HL-60	blood:	n/a	chr1:114415529-114415542 chr1:114415531-114415538
6	STAT3	chr1:114415155-114415477	MCF10A-Er-Src	breast:	n/a	n/a
7	NFIC	chr1:114413984-114415393	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:114413991-114415662	HL-60	blood:	n/a	n/a
9	NRF1	chr1:114415200-114415400	GM12878	blood:	n/a	n/a
10	CCNT2	chr1:114415260-114415406	K562	blood:	n/a	n/a
11	POLR2A	chr1:114414064-114415388	GM18505	blood:	n/a	n/a
12	RUNX3	chr1:114413782-114415505	GM12878	blood:	n/a	chr1:114413835-114413844 chr1:114413835-114413844
13	MAZ	chr1:114414084-114415455	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:114413995-114415461	GM12891	blood:	n/a	n/a
15	BHLHE40	chr1:114414984-114415382	K562	blood:	n/a	n/a
16	MAX	chr1:114414068-114415495	NB4	blood:	n/a	n/a
17	MYC	chr1:114414831-114415550	NB4	blood:	n/a	n/a
18	BHLHE40	chr1:114414155-114415413	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:114414093-114415376	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:114415204-114415404	MCF10A-Er-Src	breast:	n/a	n/a
21	REST	chr1:114414701-114415577	HL-60	blood:	n/a	n/a
22	MTA3	chr1:114413980-114415530	GM12878	blood:	n/a	n/a
23	TBP	chr1:114413826-114415380	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:114396190..114400486-chr1:114415320..114417523,4	MCF-7	breast:
2	chr1:114410354..114414312-chr1:114415133..114418521,4	K562	blood:
3	chr1:114415189..114417454-chr1:114422016..114424443,3	MCF-7	breast:
4	chr1:114414869..114417107-chr1:114504505..114506376,2	MCF-7	breast:
5	chr1:114406415..114409369-chr1:114414914..114416581,3	K562	blood:
6	chr1:114414556..114418668-chr1:114471915..114474547,3	K562	blood:
7	chr1:114403069..114405298-chr1:114414916..114416570,2	MCF-7	breast:
8	chr1:114406159..114409369-chr1:114414864..114416515,3	K562	blood:
9	chr1:114414414..114416585-chr1:114444953..114447889,2	K562	blood:

No data

Variant related genes	Relation type
PTPN22	TF binding region
ENSG00000134242	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000226167	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10858017	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10858018	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10858019	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10858021	0.82[EUR][1000 genomes]
rs11102691	0.82[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041547	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12044534	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12061482	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs12063216	0.84[EUR][1000 genomes]
rs1217376	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217377	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217380	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217388	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217389	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217395	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217396	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1217407	0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217410	0.90[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217412	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217413	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1217415	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs1217416	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1217421	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1230637	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1230638	0.83[EUR][1000 genomes]
rs1230639	0.83[EUR][1000 genomes]
rs1230640	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1230642	0.82[EUR][1000 genomes]
rs1230645	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1230646	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1230647	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs1230649	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1230656	0.86[EUR][1000 genomes]
rs1230661	0.85[EUR][1000 genomes]
rs1230678	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1230679	0.84[EUR][1000 genomes]
rs1230685	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1230687	0.83[EUR][1000 genomes]
rs1237682	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566340	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1599971	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1775754	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1935838	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1936398	0.90[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs1981319	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2093436	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2243471	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295853	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2358816	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2358994	1.00[ASW][hapmap]
rs2359167	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2488458	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636013	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2636014	0.82[EUR][1000 genomes]
rs2797408	0.84[EUR][1000 genomes]
rs2797409	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2797412	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3761936	1.00[ASW][hapmap]
rs4145859	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4423005	0.82[EUR][1000 genomes]
rs4565712	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4600045	0.90[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs61817589	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6537795	0.84[EUR][1000 genomes]
rs6663679	0.82[EUR][1000 genomes]
rs6698586	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs7529353	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7553188	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2488457	PHTF1	cis	cerebellum	SCAN
rs2488457	MAGI3	cis	parietal	SCAN
rs2488457	PHTF1	cis	parietal	SCAN
rs2488457	MAGI3	cis	cerebellum	SCAN
rs2488457	CD58	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114410000-114417800	Enhancers	NHEK	skin
2	chr1:114410800-114415600	Enhancers	HMEC	breast
3	chr1:114412000-114415600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr1:114412400-114415600	Flanking Active TSS	Dnd41	blood
5	chr1:114412600-114415600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr1:114412600-114416000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:114412600-114417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:114413000-114415400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:114413000-114415600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr1:114413200-114415600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:114413600-114415400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:114414000-114415400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:114414000-114415400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr1:114414000-114415400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:114414000-114415400	Enhancers	HSMM	muscle
16	chr1:114414000-114415600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:114414000-114415600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:114414000-114415600	Enhancers	Osteobl	bone
19	chr1:114414000-114415800	Enhancers	Adipose Nuclei	Adipose
20	chr1:114414200-114415400	Enhancers	Colonic Mucosa	Colon
21	chr1:114414200-114417600	Enhancers	HUVEC	blood vessel
22	chr1:114414400-114415400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr1:114414400-114415400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:114414400-114415400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr1:114414400-114415400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:114414400-114415600	Enhancers	Primary B cells from peripheral blood	blood
27	chr1:114414400-114415600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr1:114414400-114415600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:114414400-114415600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr1:114414400-114415600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr1:114414400-114415600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:114414400-114415600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:114414400-114415600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:114414400-114415800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr1:114414400-114415800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:114414400-114415800	Flanking Active TSS	GM12878-XiMat	blood
37	chr1:114414400-114417200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:114414600-114415400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:114414600-114415600	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:114414600-114415600	Enhancers	Small Intestine	intestine
41	chr1:114414600-114415600	Enhancers	K562	blood
42	chr1:114414800-114415600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:114415000-114415600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:114415200-114415400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:114415200-114415400	Flanking Active TSS	Fetal Thymus	thymus
47	chr1:114415200-114415400	Enhancers	Thymus	Thymus
48	chr1:114415200-114415600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr1:114415200-114416600	Weak transcription	NH-A	brain
50	chr1:114415200-114418200	Enhancers	Primary hematopoietic stem cells	blood

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