Variant report

Variant	rs1553325
Chromosome Location	chr5:75471717-75471718
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	GABPA	chr5:75471625-75471978	K562	blood:	n/a	n/a
2	EP300	chr5:75471590-75472439	K562	blood:	n/a	n/a
3	ATF2	chr5:75471604-75472348	GM12878	blood:	n/a	n/a
4	MAZ	chr5:75470941-75472282	GM12878	blood:	n/a	n/a
5	ATF3	chr5:75471599-75472016	K562	blood:	n/a	n/a
6	PAX5	chr5:75471628-75472362	GM12878	blood:	n/a	n/a
7	CEBPB	chr5:75471561-75471990	K562	blood:	n/a	n/a
8	GATA1	chr5:75471634-75472027	K562	blood:	n/a	chr5:75471846-75471863 chr5:75471841-75471857 chr5:75471845-75471854 chr5:75471844-75471854
9	CTCF	chr5:75471680-75471830	SAEC	small airway:	n/a	n/a
10	EBF1	chr5:75471716-75472261	GM12878	blood:	n/a	chr5:75471882-75471893
11	GATA2	chr5:75471512-75472088	K562	blood:	n/a	chr5:75471846-75471863 chr5:75471841-75471857 chr5:75471845-75471854 chr5:75471844-75471854
12	IRF1	chr5:75471662-75472035	K562	blood:	n/a	chr5:75471790-75471804
13	HDAC2	chr5:75471637-75471944	K562	blood:	n/a	chr5:75471844-75471853
14	NFIC	chr5:75470896-75472411	GM12878	blood:	n/a	n/a
15	CEBPD	chr5:75471616-75472089	K562	blood:	n/a	n/a
16	RAD21	chr5:75471579-75471882	GM12878	blood:	n/a	n/a
17	PML	chr5:75471635-75472087	K562	blood:	n/a	n/a
18	EP300	chr5:75471661-75472325	GM12878	blood:	n/a	n/a
19	MYC	chr5:75471553-75472063	K562	blood:	n/a	n/a
20	EP300	chr5:75471543-75471955	SK-N-SH_RA	brain:	n/a	n/a
21	IKZF1	chr5:75471645-75472516	GM12878	blood:	n/a	n/a
22	MAX	chr5:75471565-75471997	K562	blood:	n/a	n/a
23	TBL1XR1	chr5:75471670-75472025	K562	blood:	n/a	n/a
24	MYC	chr5:75471545-75472230	K562	blood:	n/a	n/a
25	BCL3	chr5:75471555-75472304	GM12878	blood:	n/a	n/a
26	REST	chr5:75471676-75471992	K562	blood:	n/a	n/a
27	RCOR1	chr5:75471582-75472103	K562	blood:	n/a	n/a
28	STAT5A	chr5:75471518-75472222	GM12878	blood:	n/a	chr5:75471928-75471940 chr5:75471546-75471553
29	MAX	chr5:75471549-75472075	K562	blood:	n/a	n/a
30	POLR2A	chr5:75471639-75472075	K562	blood:	n/a	n/a
31	GATA3	chr5:75471109-75472011	SH-SY5Y	brain:	n/a	chr5:75471846-75471863 chr5:75471841-75471857 chr5:75471845-75471854 chr5:75471844-75471854
32	JUN	chr5:75471551-75471935	K562	blood:	n/a	chr5:75471679-75471686
33	MTA3	chr5:75471526-75472401	GM12878	blood:	n/a	n/a
34	CTCF	chr5:75471620-75471770	GM12873	blood:	n/a	n/a
35	TCF3	chr5:75471615-75472016	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:75471631-75472076	K562	blood:	n/a	n/a
37	RAD21	chr5:75471586-75471914	SK-N-SH_RA	brain:	n/a	n/a
38	JUND	chr5:75471601-75472076	K562	blood:	n/a	chr5:75471679-75471686
39	NR2F2	chr5:75471579-75472045	K562	blood:	n/a	n/a
40	ELF1	chr5:75471544-75472184	GM12878	blood:	n/a	chr5:75472041-75472052
41	CTCF	chr5:75471660-75471810	BE2_C	brain:	n/a	n/a
42	MXI1	chr5:75471613-75471974	K562	blood:	n/a	n/a
43	CTCF	chr5:75471640-75471790	GM12864	blood:	n/a	n/a
44	TEAD4	chr5:75471544-75472105	K562	blood:	n/a	n/a
45	NR2F2	chr5:75471536-75472228	K562	blood:	n/a	n/a
46	RCOR1	chr5:75471558-75472234	K562	blood:	n/a	n/a
47	ATF1	chr5:75471623-75472170	K562	blood:	n/a	n/a
48	CTCF	chr5:75470750-75472090	SK-N-SH	brain:	n/a	chr5:75471073-75471082 chr5:75471062-75471083 chr5:75471067-75471085
49	PML	chr5:75471460-75472592	GM12878	blood:	n/a	n/a
50	CTCF	chr5:75471636-75471728	GM19238	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000254893	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10038253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040232	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10064352	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10066377	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10474464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514060	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10514061	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10514062	0.95[GIH][hapmap]
rs11742697	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12152728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522618	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13153946	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13155330	1.00[CHB][hapmap]
rs13158110	0.87[ASN][1000 genomes]
rs13174339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs13178459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1553324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17565925	1.00[CHB][hapmap]
rs17565946	1.00[CHB][hapmap]
rs17565960	1.00[CHB][hapmap]
rs17650942	1.00[CHB][hapmap]
rs17651115	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs17651281	1.00[JPT][hapmap]
rs1895390	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2055439	0.92[YRI][hapmap]
rs2358531	0.95[GIH][hapmap]
rs34476924	1.00[ASN][1000 genomes]
rs35357454	0.81[ASN][1000 genomes]
rs4532342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582256	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610441	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4703696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704283	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704286	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58628146	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62361382	0.87[ASN][1000 genomes]
rs62363488	0.87[ASN][1000 genomes]
rs62363490	0.87[ASN][1000 genomes]
rs6414967	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414968	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453205	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs6453206	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6453208	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6859434	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6860159	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6866404	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6868505	0.86[YRI][hapmap]
rs6881418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs72771998	0.81[ASN][1000 genomes]
rs736005	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7701465	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7710307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718358	1.00[CHB][hapmap]
rs7719752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732173	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7732692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734441	0.81[ASN][1000 genomes]
rs9293675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2757119	chr5:75426863-75474780	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv2759351	chr5:75426863-75474780	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv34958	chr5:75429015-75474921	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1553325	METTL7A	trans	cerebellum	SCAN
rs1553325	FCHO2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75470600-75472200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr5:75470600-75472600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:75470600-75472800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:75470600-75476400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:75470800-75472600	Enhancers	Primary B cells from peripheral blood	blood
6	chr5:75471000-75472000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:75471000-75472200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:75471000-75472600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr5:75471000-75472600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr5:75471000-75474200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:75471200-75471800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr5:75471200-75471800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:75471200-75472000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr5:75471200-75472000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:75471200-75472200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:75471200-75472200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:75471200-75472200	Flanking Active TSS	K562	blood
18	chr5:75471200-75472400	Enhancers	Primary B cells from cord blood	blood
19	chr5:75471200-75472600	Enhancers	Primary T cells from cord blood	blood
20	chr5:75471200-75472600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr5:75471200-75472600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr5:75471200-75472600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr5:75471200-75472600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr5:75471200-75472600	Flanking Active TSS	GM12878-XiMat	blood
25	chr5:75471200-75472600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:75471400-75471800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr5:75471400-75471800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr5:75471400-75472200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr5:75471600-75471800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:75471600-75471800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr5:75471600-75471800	Enhancers	Duodenum Mucosa	Duodenum
32	chr5:75471600-75472000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:75471600-75472000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:75471600-75472000	Enhancers	Fetal Thymus	thymus
35	chr5:75471600-75472200	Enhancers	Dnd41	blood

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