Variant report

Variant	rs4704333
Chromosome Location	chr5:75842335-75842336
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	MTA3	chr5:75842104-75844288	GM12878	blood:	n/a	n/a
2	CHD2	chr5:75842229-75844299	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:75842198-75842994	GM12891	blood:	n/a	n/a
4	SP1	chr5:75842196-75842973	GM12878	blood:	n/a	n/a
5	RUNX3	chr5:75842189-75842906	GM12878	blood:	n/a	n/a
6	BHLHE40	chr5:75842244-75843807	GM12878	blood:	n/a	n/a
7	NFATC1	chr5:75842251-75842839	GM12878	blood:	n/a	n/a
8	MTA3	chr5:75842283-75843064	GM12878	blood:	n/a	n/a
9	IRF4	chr5:75842330-75842988	GM12878	blood:	n/a	n/a
10	RUNX3	chr5:75842112-75843749	GM12878	blood:	n/a	chr5:75843370-75843379 chr5:75843370-75843379
11	TCF3	chr5:75842120-75842965	GM12878	blood:	n/a	n/a
12	TBP	chr5:75842238-75843640	GM12878	blood:	n/a	n/a
13	CREB1	chr5:75842171-75843766	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr5:75842254-75843581	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:75842276-75843059	GM12892	blood:	n/a	n/a
16	TCF12	chr5:75842292-75842842	GM12878	blood:	n/a	n/a
17	NFIC	chr5:75842272-75843807	GM12878	blood:	n/a	n/a
18	MXI1	chr5:75842230-75843966	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:75842274-75843535	GM12878	blood:	n/a	n/a
20	EP300	chr5:75842280-75842933	GM12878	blood:	n/a	chr5:75842431-75842445
21	PAX5	chr5:75842107-75843023	GM12878	blood:	n/a	chr5:75842697-75842706 chr5:75842793-75842803 chr5:75842758-75842767 chr5:75842431-75842440 chr5:75842444-75842453
22	ATF2	chr5:75842225-75843735	GM12878	blood:	n/a	n/a
23	SP1	chr5:75842137-75842944	GM12878	blood:	n/a	n/a
24	EP300	chr5:75842174-75843737	GM12878	blood:	n/a	chr5:75842431-75842445
25	POLR2A	chr5:75842228-75843863	GM12878	blood:	n/a	n/a
26	CREB1	chr5:75842110-75843015	GM12878	blood:	n/a	n/a
27	EP300	chr5:75842171-75843681	GM12878	blood:	n/a	chr5:75842431-75842445
28	POLR2A	chr5:75842273-75843040	GM12891	blood:	n/a	n/a
29	ZNF384	chr5:75842228-75842936	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10041515	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10043064	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10044679	0.86[AMR][1000 genomes]
rs10044688	0.88[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10051729	0.86[AMR][1000 genomes]
rs10054114	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10064543	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs10065424	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073592	0.82[AMR][1000 genomes]
rs10080190	0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10474482	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10942784	0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12513951	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13355881	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1501690	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2047731	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2134190	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2173926	0.81[EUR][1000 genomes]
rs2202113	0.89[JPT][hapmap]
rs2202114	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840106	0.82[EUR][1000 genomes]
rs2884654	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3776768	0.81[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs3797380	0.88[JPT][hapmap]
rs4235700	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4437351	0.82[AMR][1000 genomes]
rs4704326	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4704330	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704336	0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6453231	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6453232	0.93[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6869692	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6889411	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7707801	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713954	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7722711	0.94[JPT][hapmap]
rs905162	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs905163	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs905164	0.81[GIH][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9293687	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]
rs9293688	0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs9686939	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4704333	GFM2	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75837400-75842800	Enhancers	Liver	Liver
3	chr5:75839400-75842400	Weak transcription	Adipose Nuclei	Adipose
4	chr5:75839400-75842600	Weak transcription	Thymus	Thymus
5	chr5:75839600-75845400	Enhancers	HepG2	liver
6	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr5:75840000-75842400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:75840000-75842600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr5:75840200-75842400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:75840200-75842400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:75840200-75842400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:75840200-75842400	Weak transcription	Colonic Mucosa	Colon
14	chr5:75840200-75842400	Weak transcription	Fetal Stomach	stomach
15	chr5:75840200-75842400	Weak transcription	Gastric	stomach
16	chr5:75840200-75842400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:75840200-75842400	Weak transcription	Small Intestine	intestine
18	chr5:75840200-75842600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr5:75840200-75842800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:75840200-75842800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr5:75840200-75842800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr5:75840200-75842800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:75840200-75842800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:75840200-75843200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:75840400-75842400	Weak transcription	Lung	lung
26	chr5:75840400-75842400	Weak transcription	Spleen	Spleen
27	chr5:75840400-75842800	Enhancers	Primary hematopoietic stem cells	blood
28	chr5:75840400-75843000	Weak transcription	Fetal Intestine Large	intestine
29	chr5:75840400-75843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:75840600-75842400	Weak transcription	Fetal Kidney	kidney
31	chr5:75840600-75842600	Weak transcription	Fetal Lung	lung
32	chr5:75840600-75843000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:75841000-75843200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:75841200-75842400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:75841200-75842400	Weak transcription	Placenta	Placenta
36	chr5:75841200-75842400	Weak transcription	K562	blood
37	chr5:75841200-75842600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:75841200-75843000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr5:75841400-75842400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:75841400-75842400	Weak transcription	Fetal Intestine Small	intestine
41	chr5:75841400-75842800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:75841800-75842800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr5:75841800-75843000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr5:75841800-75843000	Enhancers	Primary B cells from cord blood	blood
45	chr5:75842000-75842600	Enhancers	Esophagus	oesophagus
46	chr5:75842000-75842600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr5:75842000-75842800	Enhancers	Duodenum Mucosa	Duodenum
48	chr5:75842000-75843000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr5:75842000-75843800	Enhancers	Fetal Muscle Leg	muscle
50	chr5:75842000-75844600	Enhancers	Primary B cells from peripheral blood	blood

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