Variant report

Variant	rs9293687
Chromosome Location	chr5:75839124-75839125
allele	A/G
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	chr5:75838483-75840557	PBDE	blood:	n/a	n/a
2	STAT2	chr5:75838721-75839133	K562	blood:	n/a	n/a
3	RUNX3	chr5:75838732-75839565	GM12878	blood:	n/a	n/a
4	TEAD4	chr5:75838470-75839588	K562	blood:	n/a	n/a
5	UBTF	chr5:75838914-75839480	K562	blood:	n/a	n/a
6	CEBPB	chr5:75838729-75839173	K562	blood:	n/a	n/a
7	GATA1	chr5:75838187-75839958	K562	blood:	n/a	chr5:75839479-75839486 chr5:75839472-75839493 chr5:75839477-75839489 chr5:75838499-75838509 chr5:75839475-75839491 chr5:75838896-75838913 chr5:75839479-75839486 chr5:75839475-75839491 chr5:75839479-75839486 chr5:75839479-75839488 chr5:75839478-75839488
8	CEBPD	chr5:75838593-75839178	K562	blood:	n/a	n/a
9	MAX	chr5:75838696-75839553	NB4	blood:	n/a	n/a
10	MAX	chr5:75838845-75839538	K562	blood:	n/a	n/a
11	MYC	chr5:75839040-75839144	K562	blood:	n/a	n/a
12	MAZ	chr5:75838607-75839518	K562	blood:	n/a	n/a
13	NFIC	chr5:75838726-75839300	GM12878	blood:	n/a	n/a
14	ATF1	chr5:75838766-75839534	K562	blood:	n/a	n/a
15	RUNX3	chr5:75838669-75839605	GM12878	blood:	n/a	n/a
16	EP300	chr5:75838659-75839600	K562	blood:	n/a	n/a
17	MTA3	chr5:75838802-75839518	GM12878	blood:	n/a	n/a
18	GATA1	chr5:75838375-75839559	PBDE	blood:	n/a	chr5:75839479-75839486 chr5:75839472-75839493 chr5:75839477-75839489 chr5:75838499-75838509 chr5:75839475-75839491 chr5:75838896-75838913 chr5:75839479-75839486 chr5:75839475-75839491 chr5:75839479-75839486 chr5:75839479-75839488 chr5:75839478-75839488
19	MYC	chr5:75838759-75839542	K562	blood:	n/a	n/a
20	CEBPB	chr5:75838629-75839189	K562	blood:	n/a	n/a
21	BHLHE40	chr5:75839001-75839405	GM12878	blood:	n/a	n/a
22	CCNT2	chr5:75838441-75839406	K562	blood:	n/a	chr5:75838896-75838916
23	ATF2	chr5:75838932-75839432	GM12878	blood:	n/a	n/a
24	CEBPD	chr5:75838740-75839199	K562	blood:	n/a	n/a
25	UBTF	chr5:75838923-75839414	K562	blood:	n/a	n/a
26	RCOR1	chr5:75838076-75839656	K562	blood:	n/a	n/a
27	JUND	chr5:75838714-75839487	K562	blood:	n/a	n/a

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10041515	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10043064	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10044688	0.88[CEU][hapmap];0.84[CHB][hapmap];0.96[GIH][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10054114	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10064543	0.85[CHB][hapmap]
rs10065424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10080190	0.82[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10942784	0.88[CHB][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12513951	0.85[CHB][hapmap]
rs13355881	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1501690	0.84[EUR][1000 genomes]
rs2047731	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2134190	0.82[EUR][1000 genomes]
rs2173926	0.81[EUR][1000 genomes]
rs2202114	0.88[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2840106	0.83[EUR][1000 genomes]
rs2884654	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3776768	0.81[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs4235700	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704326	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4704330	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4704332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704336	0.81[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6453231	0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6453232	0.93[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6869692	0.81[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7707801	0.92[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7713954	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs905162	0.83[EUR][1000 genomes]
rs905163	0.81[EUR][1000 genomes]
rs905164	0.81[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9293688	0.85[CHB][hapmap]
rs9686939	0.95[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[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	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS 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	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9293687	GFM2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75806800-75839200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:75826800-75840000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:75830000-75841600	Enhancers	Stomach Mucosa	stomach
4	chr5:75832200-75840000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:75833600-75839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:75834000-75839200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr5:75834200-75839200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:75834400-75839200	Weak transcription	Fetal Intestine Small	intestine
9	chr5:75835600-75839800	Weak transcription	Spleen	Spleen
10	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:75836600-75839200	Weak transcription	Pancreas	Pancrea
12	chr5:75836600-75839600	Weak transcription	HepG2	liver
13	chr5:75837400-75840600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:75837400-75842800	Enhancers	Liver	Liver
15	chr5:75837800-75840600	Enhancers	Fetal Lung	lung
16	chr5:75837800-75841200	Enhancers	Placenta	Placenta
17	chr5:75838000-75840400	Enhancers	Fetal Thymus	thymus
18	chr5:75838000-75840600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:75838200-75840200	Enhancers	Small Intestine	intestine
20	chr5:75838200-75840600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr5:75838200-75841400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:75838400-75839200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:75838400-75839400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:75838400-75840200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr5:75838400-75840200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:75838400-75840600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr5:75838400-75840600	Enhancers	Fetal Kidney	kidney
28	chr5:75838600-75839400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr5:75838600-75839400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr5:75838600-75839600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr5:75838600-75839600	Enhancers	Fetal Stomach	stomach
32	chr5:75838600-75840000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr5:75838600-75840200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr5:75838600-75840400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr5:75838600-75840400	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr5:75838600-75840600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:75838800-75839200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr5:75838800-75839400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr5:75838800-75839400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr5:75838800-75839400	Active TSS	Adipose Nuclei	Adipose
41	chr5:75838800-75839400	Enhancers	Thymus	Thymus
42	chr5:75838800-75839400	Flanking Active TSS	K562	blood
43	chr5:75838800-75839600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr5:75838800-75839600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:75838800-75839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:75838800-75839800	Flanking Active TSS	GM12878-XiMat	blood
47	chr5:75838800-75840200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr5:75838800-75840200	Enhancers	Gastric	stomach
49	chr5:75839000-75839200	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr5:75839000-75839400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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