Variant report

Variant	rs3776984
Chromosome Location	chr5:154236694-154236695
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	POLR2A	chr5:154236302-154238925	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr5:154236644-154238345	H1-neurons	neurons:	n/a	n/a
3	EP300	chr5:154236608-154238758	K562	blood:	n/a	n/a
4	SMARCC1	chr5:154236659-154238334	Hela-S3	cervix:	n/a	n/a
5	SIN3AK20	chr5:154236640-154238540	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr5:154236415-154240199	IMR90	lung:	n/a	chr5:154237410-154237425 chr5:154237408-154237423
7	POLR2A	chr5:154236659-154238472	K562	blood:	n/a	n/a
8	BCL3	chr5:154236466-154238491	A549	lung:	n/a	chr5:154238233-154238246
9	POLR2A	chr5:154236365-154239243	SK-N-MC	brain:	n/a	n/a
10	REST	chr5:154236473-154238831	A549	lung:	n/a	chr5:154237237-154237250 chr5:154238006-154238019
11	POLR2A	chr5:154236641-154238420	K562	blood:	n/a	n/a
12	GTF2F1	chr5:154236657-154238264	Hela-S3	cervix:	n/a	n/a
13	JUND	chr5:154236588-154238797	K562	blood:	n/a	n/a
14	MXI1	chr5:154236687-154239470	GM12878	blood:	n/a	chr5:154237410-154237425 chr5:154237408-154237423
15	MAX	chr5:154236632-154238271	SK-N-SH	brain:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
16	TBP	chr5:154236649-154238717	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF7L2	chr5:154236611-154237789	Hela-S3	cervix:	n/a	n/a
18	UBTF	chr5:154236602-154237466	K562	blood:	n/a	n/a
19	TEAD4	chr5:154236474-154238354	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr5:154236656-154239951	GM12891	blood:	n/a	n/a
21	TEAD4	chr5:154236594-154238352	K562	blood:	n/a	n/a
22	MAX	chr5:154236621-154238433	ECC-1	luminal epithelium:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
23	CBX3	chr5:154236588-154238341	K562	blood:	n/a	chr5:154236872-154236883
24	TCF7L2	chr5:154236533-154238372	HEK293	kidney:	n/a	n/a
25	E2F4	chr5:154236612-154237501	Hela-S3	cervix:	n/a	chr5:154237058-154237067 chr5:154237334-154237343
26	MAZ	chr5:154236459-154240485	IMR90	lung:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
27	ATF2	chr5:154236539-154236844	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr5:154236669-154238491	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF7L2	chr5:154236481-154239255	Hela-S3	cervix:	n/a	chr5:154238363-154238377
30	HEY1	chr5:154236522-154238510	HepG2	liver:	n/a	n/a
31	MTA3	chr5:154236481-154239350	GM12878	blood:	n/a	n/a
32	KAP1	chr5:154236519-154238146	U2OS	brain:	n/a	n/a
33	POLR2A	chr5:154236581-154238523	H1-neurons	neurons:	n/a	n/a
34	MAX	chr5:154236628-154238504	MCF-7	breast:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
35	SIN3AK20	chr5:154236423-154238605	MCF-7	breast:	n/a	n/a
36	POLR2A	chr5:154236504-154238502	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr5:154236599-154238587	Hela-S3	cervix:	n/a	n/a
38	ZNF384	chr5:154235497-154238305	K562	blood:	n/a	n/a
39	USF2	chr5:154236629-154236840	Hela-S3	cervix:	n/a	n/a
40	MYC	chr5:154236613-154238262	K562	blood:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
41	MYC	chr5:154236490-154238760	K562	blood:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
42	POLR2A	chr5:154236682-154239046	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr5:154236531-154238419	K562	blood:	n/a	n/a
44	MAX	chr5:154236672-154238328	H1-hESC	embryonic stem cell:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
45	CREB1	chr5:154236608-154238421	K562	blood:	n/a	n/a
46	PML	chr5:154236480-154238486	K562	blood:	n/a	chr5:154238450-154238458
47	E2F6	chr5:154236617-154237535	H1-hESC	embryonic stem cell:	n/a	chr5:154237058-154237067 chr5:154237334-154237343
48	TCF7L2	chr5:154236493-154238620	HCT-116	colon:	n/a	chr5:154238363-154238377
49	MAX	chr5:154236474-154238928	A549	lung:	n/a	chr5:154237003-154237012 chr5:154237410-154237419 chr5:154237666-154237676
50	HA-E2F1	chr5:154236641-154238505	MCF-7	breast:	n/a	chr5:154237058-154237067 chr5:154237970-154237982 chr5:154237334-154237343 chr5:154238015-154238030

No.	Distal block	Cell Line	Cell type
1	chr5:154212721..154214972-chr5:154234901..154239444,4	K562	blood:
2	chr5:154206588..154209257-chr5:154235210..154237943,2	K562	blood:
3	chr5:154214026..154216712-chr5:154234654..154237422,2	K562	blood:
4	chr5:154133224..154141155-chr5:154235246..154242227,24	MCF-7	breast:
5	chr17:57921528..57925294-chr5:154236694..154239255,3	MCF-7	breast:
6	chr5:154228281..154231986-chr5:154234217..154239374,12	MCF-7	breast:
7	chr5:154133665..154137234-chr5:154235811..154241105,6	MCF-7	breast:
8	chr5:154236188..154239312-chr5:154315571..154321975,7	MCF-7	breast:
9	chr5:154133563..154137747-chr5:154235219..154239187,9	K562	blood:
10	chr5:154133598..154138734-chr5:154235660..154239806,12	K562	blood:
11	chr5:154224707..154230790-chr5:154235604..154239293,10	K562	blood:
12	chr5:154235909..154239670-chr5:154316883..154321797,7	K562	blood:
13	chr5:154235585..154240256-chr5:154317008..154321464,8	K562	blood:
14	chr5:154189092..154191650-chr5:154236048..154238610,3	MCF-7	breast:
15	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:

Variant related genes	Relation type
CNOT8	TF binding region
ENSG00000155506	Chromatin interaction
ENSG00000082516	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000170271	Chromatin interaction
ENSG00000263361	Chromatin interaction
ENSG00000082515	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1035368	1.00[TSI][hapmap]
rs10515727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12186480	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12186610	0.85[EUR][1000 genomes]
rs12187572	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187890	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12187921	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12187934	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12187974	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188149	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188498	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12189508	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12300	0.90[TSI][hapmap]
rs1421813	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1421819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17096232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116409	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17116417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116421	1.00[TSI][hapmap]
rs17116433	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17116442	1.00[TSI][hapmap]
rs17116455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116534	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs17116638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17116669	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116707	1.00[JPT][hapmap]
rs1974776	1.00[TSI][hapmap]
rs1974777	1.00[TSI][hapmap]
rs2047305	1.00[JPT][hapmap]
rs2112223	1.00[CHB][hapmap]
rs2258437	1.00[TSI][hapmap]
rs2291780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2544880	1.00[TSI][hapmap]
rs2544884	1.00[TSI][hapmap]
rs2644743	1.00[TSI][hapmap]
rs2644744	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs2688198	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2688201	1.00[TSI][hapmap]
rs2688208	1.00[CHB][hapmap]
rs28372688	0.93[ASN][1000 genomes]
rs348739	1.00[TSI][hapmap]
rs348750	1.00[TSI][hapmap]
rs348752	1.00[TSI][hapmap]
rs39614	1.00[TSI][hapmap]
rs4452598	0.86[EUR][1000 genomes]
rs4626377	0.86[EUR][1000 genomes]
rs55692274	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56773390	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56895891	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61145644	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580123	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6865950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6871813	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6895588	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6895702	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6895741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs702742	1.00[TSI][hapmap]
rs73806917	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73807206	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807207	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807213	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73807216	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73809507	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7709899	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7716019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs816717	1.00[TSI][hapmap]
rs816718	1.00[CHB][hapmap];0.95[TSI][hapmap]
rs816720	1.00[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154230200-154236800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:154236200-154236800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:154236200-154237400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr5:154236200-154238800	Active TSS	Brain Germinal Matrix	brain
5	chr5:154236200-154240600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:154236400-154236800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:154236400-154236800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:154236400-154236800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:154236400-154236800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:154236400-154236800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr5:154236400-154236800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:154236400-154236800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:154236400-154236800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:154236400-154236800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:154236400-154236800	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr5:154236400-154236800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr5:154236400-154236800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr5:154236400-154236800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr5:154236400-154236800	Flanking Active TSS	Fetal Brain Female	brain
20	chr5:154236400-154236800	Flanking Active TSS	Fetal Kidney	kidney
21	chr5:154236400-154236800	Enhancers	Gastric	stomach
22	chr5:154236400-154236800	Enhancers	Pancreas	Pancrea
23	chr5:154236400-154236800	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr5:154236400-154236800	Flanking Active TSS	A549	lung
25	chr5:154236400-154236800	Flanking Active TSS	Hela-S3	cervix
26	chr5:154236400-154236800	Flanking Active TSS	HepG2	liver
27	chr5:154236400-154236800	Flanking Active TSS	HSMM	muscle
28	chr5:154236400-154236800	Flanking Active TSS	NHDF-Ad	bronchial
29	chr5:154236400-154237000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:154236400-154237000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:154236400-154237000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr5:154236400-154237000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr5:154236400-154237000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:154236400-154237000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr5:154236400-154237000	Flanking Active TSS	Fetal Lung	lung
36	chr5:154236400-154237000	Flanking Active TSS	Fetal Stomach	stomach
37	chr5:154236400-154237000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr5:154236400-154237000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr5:154236400-154237000	Flanking Active TSS	Dnd41	blood
40	chr5:154236400-154237000	Flanking Active TSS	HUVEC	blood vessel
41	chr5:154236400-154237000	Flanking Active TSS	K562	blood
42	chr5:154236400-154237000	Flanking Active TSS	NH-A	brain
43	chr5:154236400-154237000	Flanking Active TSS	NHEK	skin
44	chr5:154236400-154237000	Flanking Active TSS	Osteobl	bone
45	chr5:154236400-154237400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr5:154236400-154237400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:154236400-154237400	Flanking Active TSS	HMEC	breast
48	chr5:154236400-154237600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:154236400-154239000	Active TSS	Brain Anterior Caudate	brain
50	chr5:154236400-154239000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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