Variant report

Variant	rs2688228
Chromosome Location	chr4:8421345-8421346
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	NFE2	chr4:8421168-8421517	K562	blood:	n/a	chr4:8421327-8421342
2	NFATC1	chr4:8421064-8421678	GM12878	blood:	n/a	n/a
3	MYC	chr4:8421188-8421515	MCF10A-Er-Src	breast:	n/a	n/a
4	MAZ	chr4:8421271-8421470	GM12878	blood:	n/a	n/a
5	RELA	chr4:8421194-8421810	GM15510	blood:	n/a	chr4:8421605-8421614 chr4:8421605-8421614
6	STAT3	chr4:8421237-8421619	GM12878	blood:	n/a	n/a
7	FOS	chr4:8421170-8421677	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr4:8421179-8421624	GM12878	blood:	n/a	n/a
9	BACH1	chr4:8421183-8421487	K562	blood:	n/a	n/a
10	BACH1	chr4:8421214-8421458	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOS	chr4:8421154-8421694	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr4:8421266-8421691	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr4:8421221-8421519	K562	blood:	n/a	n/a
14	PAX5	chr4:8421291-8421622	GM12878	blood:	n/a	n/a
15	CREB1	chr4:8421068-8421872	GM12878	blood:	n/a	n/a
16	RCOR1	chr4:8421183-8421365	GM12878	blood:	n/a	n/a
17	FOS	chr4:8421140-8421587	MCF10A-Er-Src	breast:	n/a	n/a
18	EP300	chr4:8421190-8421786	GM12878	blood:	n/a	n/a
19	SP1	chr4:8421167-8421622	GM12878	blood:	n/a	n/a
20	RELA	chr4:8421246-8421773	GM19099	blood:	n/a	chr4:8421605-8421614 chr4:8421605-8421614
21	ATF2	chr4:8421154-8421641	GM12878	blood:	n/a	n/a
22	MAX	chr4:8421238-8421426	NB4	blood:	n/a	n/a
23	MYC	chr4:8421179-8421510	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr4:8421130-8421531	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:8421326-8421496	GM12878	blood:	n/a	n/a
26	CREB1	chr4:8421142-8421716	GM12878	blood:	n/a	n/a
27	CEBPB	chr4:8421010-8421474	IMR90	lung:	n/a	n/a
28	MAFK	chr4:8421147-8421533	K562	blood:	n/a	chr4:8421327-8421342
29	ATF2	chr4:8421093-8421717	GM12878	blood:	n/a	n/a
30	YY1	chr4:8421185-8421551	GM12878	blood:	n/a	n/a
31	EP300	chr4:8421217-8421718	GM12878	blood:	n/a	n/a
32	FOXA1	chr4:8421202-8421384	T-47D	breast:	n/a	n/a
33	BHLHE40	chr4:8421201-8421716	GM12878	blood:	n/a	n/a
34	TBP	chr4:8421170-8421585	GM12878	blood:	n/a	n/a
35	MAFF	chr4:8421147-8421524	K562	blood:	n/a	chr4:8421326-8421344
36	EBF1	chr4:8421171-8421714	GM12878	blood:	n/a	n/a
37	YY1	chr4:8421190-8421504	GM12892	blood:	n/a	n/a
38	IRF4	chr4:8421137-8421682	GM12878	blood:	n/a	n/a
39	NR3C1	chr4:8421200-8421583	A549	lung:	n/a	n/a
40	MAFK	chr4:8421168-8421531	IMR90	lung:	n/a	chr4:8421327-8421342
41	RELA	chr4:8421141-8421933	GM18505	blood:	n/a	chr4:8421605-8421614 chr4:8421605-8421614
42	TAL1	chr4:8421329-8421418	K562	blood:	n/a	n/a
43	NFIC	chr4:8421057-8421743	GM12878	blood:	n/a	n/a
44	BATF	chr4:8421176-8421733	GM12878	blood:	n/a	n/a
45	CHD2	chr4:8421279-8421621	GM12878	blood:	n/a	n/a
46	MAFF	chr4:8421164-8421499	HepG2	liver:	n/a	chr4:8421326-8421344
47	BCL11A	chr4:8421129-8421607	GM12878	blood:	n/a	n/a
48	MAFK	chr4:8421164-8421515	HepG2	liver:	n/a	chr4:8421327-8421342
49	TBL1XR1	chr4:8421290-8421680	GM12878	blood:	n/a	n/a
50	BHLHE40	chr4:8421192-8421946	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8419092..8423241-chr4:8430004..8433236,3	MCF-7	breast:
2	chr4:8268685..8271204-chr4:8420095..8422355,2	MCF-7	breast:

Variant related genes	Relation type
ACOX3	TF binding region
ENSG00000087008	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11729265	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12503034	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880025	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2002860	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049302	0.99[ASN][1000 genomes]
rs2140336	0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2245515	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245809	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2386223	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631723	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2631724	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2631727	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631728	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631729	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631730	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631733	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631737	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631750	0.83[ASN][1000 genomes]
rs2631752	0.92[ASN][1000 genomes]
rs2631757	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631763	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2631764	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631765	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2631766	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631767	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2631769	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688221	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688229	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688234	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688239	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2688240	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2688244	0.96[ASN][1000 genomes]
rs2688246	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103090	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3103098	0.86[JPT][hapmap]
rs3115396	0.88[EUR][1000 genomes]
rs3775893	0.87[EUR][1000 genomes]
rs4325994	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56343159	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs954270	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954271	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv593639	chr4:8394376-8424108	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv964028	chr4:8418957-8430160	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2688228	TBC1D14	cis	parietal	SCAN
rs2688228	C4orf23	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8399600-8429400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:8404600-8429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:8408800-8422400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:8412800-8425600	Weak transcription	Fetal Heart	heart
5	chr4:8413000-8423400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:8416400-8421400	Weak transcription	HSMM	muscle
7	chr4:8416400-8428000	Weak transcription	Fetal Brain Male	brain
8	chr4:8416800-8421400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:8416800-8429000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:8416800-8429000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:8416800-8429000	Weak transcription	Fetal Kidney	kidney
12	chr4:8416800-8429000	Weak transcription	HUVEC	blood vessel
13	chr4:8417000-8421600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:8417000-8428400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:8417000-8429000	Weak transcription	Small Intestine	intestine
16	chr4:8417600-8428800	Weak transcription	Dnd41	blood
17	chr4:8417800-8421400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:8417800-8421400	Weak transcription	NH-A	brain
19	chr4:8417800-8428400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:8417800-8428800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:8417800-8428800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:8417800-8429000	Weak transcription	Primary B cells from cord blood	blood
23	chr4:8417800-8429000	Weak transcription	Colonic Mucosa	Colon
24	chr4:8417800-8429000	Weak transcription	HSMMtube	muscle
25	chr4:8417800-8429200	Weak transcription	Fetal Lung	lung
26	chr4:8418000-8421400	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:8418000-8421400	Weak transcription	Left Ventricle	heart
28	chr4:8418000-8428400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:8418000-8428800	Weak transcription	Stomach Mucosa	stomach
30	chr4:8418000-8429000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:8418000-8429000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:8418000-8429000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr4:8418200-8421400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:8418200-8421400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:8418200-8421400	Weak transcription	Adipose Nuclei	Adipose
36	chr4:8418200-8421400	Weak transcription	Right Ventricle	heart
37	chr4:8418200-8421400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:8418200-8422000	Weak transcription	Ovary	ovary
39	chr4:8418200-8425800	Weak transcription	Brain Anterior Caudate	brain
40	chr4:8418200-8428000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:8418200-8428800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:8418200-8429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr4:8418200-8429000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:8418400-8427800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr4:8418400-8428000	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:8418400-8428400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:8418400-8428800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr4:8418400-8429000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:8418400-8429000	Weak transcription	NHEK	skin
50	chr4:8418600-8421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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