Variant report

Variant	rs3776601
Chromosome Location	chr5:92925443-92925444
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	RAD21	chr5:92925439-92925738	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr5:92925431-92925683	HepG2	liver:	n/a	n/a
3	RAD21	chr5:92925211-92925809	IMR90	lung:	n/a	n/a
4	CTCF	chr5:92925380-92925670	HCPEpiC	choroid plexus:	n/a	n/a
5	CTCF	chr5:92925360-92925510	HPF	lung:	n/a	n/a
6	RAD21	chr5:92925290-92926168	SK-N-SH	brain:	n/a	n/a
7	CHD1	chr5:92912776-92927520	IMR90	lung:	n/a	chr5:92914877-92914887 chr5:92926304-92926314 chr5:92917311-92917321 chr5:92918655-92918665 chr5:92918684-92918694 chr5:92920697-92920707 chr5:92920384-92920394 chr5:92915468-92915478 chr5:92917327-92917337 chr5:92920376-92920386
8	POLR2A	chr5:92924900-92928001	U87	brain:	n/a	n/a
9	POLR2A	chr5:92924657-92925465	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:92925322..92926942-chr5:92936051..92937789,2	MCF-7	breast:

Variant related genes	Relation type
NR2F1	TF binding region
NR2F1-AS1	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10038831	0.86[JPT][hapmap]
rs10041792	0.86[JPT][hapmap]
rs1004941	0.86[JPT][hapmap]
rs10050364	0.84[JPT][hapmap]
rs10051878	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10060331	0.86[JPT][hapmap]
rs10067541	0.86[JPT][hapmap]
rs10071040	0.86[JPT][hapmap]
rs1038686	0.86[JPT][hapmap]
rs1046217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10476520	0.86[JPT][hapmap]
rs10514376	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12186735	0.86[ASN][1000 genomes]
rs12187239	0.93[ASN][1000 genomes]
rs12188716	0.86[ASN][1000 genomes]
rs12188905	0.93[ASN][1000 genomes]
rs13154650	0.86[JPT][hapmap]
rs13161885	0.86[JPT][hapmap]
rs17082127	0.86[ASN][1000 genomes]
rs17082129	0.86[ASN][1000 genomes]
rs17083181	0.86[ASN][1000 genomes]
rs17083191	0.93[ASN][1000 genomes]
rs17083194	0.93[ASN][1000 genomes]
rs17083198	0.93[ASN][1000 genomes]
rs17083200	0.93[ASN][1000 genomes]
rs17083213	0.93[ASN][1000 genomes]
rs17083228	0.93[ASN][1000 genomes]
rs17083278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17083297	0.86[JPT][hapmap]
rs17312456	0.86[JPT][hapmap]
rs17370695	0.86[ASN][1000 genomes]
rs17372615	0.86[JPT][hapmap]
rs1824153	0.86[ASN][1000 genomes]
rs1844343	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs2083227	0.86[ASN][1000 genomes]
rs2279473	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57690257	0.86[ASN][1000 genomes]
rs58143801	0.80[ASN][1000 genomes]
rs58237393	0.80[ASN][1000 genomes]
rs59360932	0.93[ASN][1000 genomes]
rs61324921	0.86[ASN][1000 genomes]
rs61352323	0.93[ASN][1000 genomes]
rs61429325	0.80[ASN][1000 genomes]
rs6556823	0.86[ASN][1000 genomes]
rs6556824	0.93[ASN][1000 genomes]
rs6556828	0.86[JPT][hapmap]
rs6556829	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6556834	0.86[JPT][hapmap]
rs6866771	0.93[ASN][1000 genomes]
rs6877616	0.86[JPT][hapmap]
rs6879620	0.86[JPT][hapmap]
rs6879816	0.93[ASN][1000 genomes]
rs6880843	0.86[ASN][1000 genomes]
rs6881815	0.86[JPT][hapmap]
rs6884138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6889857	0.93[ASN][1000 genomes]
rs6890998	0.86[JPT][hapmap]
rs6892853	0.80[ASN][1000 genomes]
rs6895356	0.86[JPT][hapmap]
rs6898507	0.86[JPT][hapmap]
rs73133228	0.86[ASN][1000 genomes]
rs73133239	0.86[ASN][1000 genomes]
rs73133251	0.93[ASN][1000 genomes]
rs73133261	0.93[ASN][1000 genomes]
rs73133265	0.93[ASN][1000 genomes]
rs73133275	0.93[ASN][1000 genomes]
rs73133278	0.93[ASN][1000 genomes]
rs73133280	0.93[ASN][1000 genomes]
rs73133282	0.93[ASN][1000 genomes]
rs73133283	0.93[ASN][1000 genomes]
rs73133287	0.93[ASN][1000 genomes]
rs73133289	0.93[ASN][1000 genomes]
rs73133292	0.93[ASN][1000 genomes]
rs73133301	0.93[ASN][1000 genomes]
rs73135320	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135321	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73772907	0.89[ASN][1000 genomes]
rs7702348	0.86[JPT][hapmap]
rs7702649	0.86[JPT][hapmap]
rs7712388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7712899	0.93[ASN][1000 genomes]
rs7717718	0.86[JPT][hapmap]
rs7721168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7721509	1.00[CHB][hapmap]
rs7727107	0.93[ASN][1000 genomes]
rs7736624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9314086	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451945	chr5:92858750-93024740	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv830404	chr5:92868336-93048257	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv1819334	chr5:92892591-92956733	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv882383	chr5:92895401-92928346	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv823130	chr5:92896346-92966016	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv4918	chr5:92898426-92943359	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv823132	chr5:92898512-92969668	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1794960	chr5:92919821-92932305	Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1837322	chr5:92919821-92933747	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3350173	chr5:92923496-92925444	Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:92914000-92925800	Active TSS	Brain Angular Gyrus	brain
2	chr5:92914200-92926200	Active TSS	Fetal Brain Female	brain
3	chr5:92914800-92926000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:92916200-92927600	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr5:92920800-92929400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:92921000-92927800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:92922200-92931400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:92922200-92934200	Weak transcription	HSMMtube	muscle
9	chr5:92922600-92929200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:92922800-92927000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
11	chr5:92922800-92927800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:92922800-92929800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:92923400-92928000	Transcr. at gene 5' and 3'	NHLF	lung
14	chr5:92924000-92926000	Active TSS	Brain Anterior Caudate	brain
15	chr5:92924200-92926800	Weak transcription	Liver	Liver
16	chr5:92924200-92929400	Weak transcription	HMEC	breast
17	chr5:92924200-92935000	Weak transcription	Gastric	stomach
18	chr5:92924400-92929800	Weak transcription	NHDF-Ad	bronchial
19	chr5:92924600-92926000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:92924600-92926000	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
21	chr5:92924600-92926200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
22	chr5:92924600-92926400	Active TSS	Stomach Smooth Muscle	stomach
23	chr5:92924600-92927000	Enhancers	HUVEC	blood vessel
24	chr5:92924600-92927600	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
25	chr5:92924600-92928600	Weak transcription	Adipose Nuclei	Adipose
26	chr5:92924600-92930600	Weak transcription	Pancreas	Pancrea
27	chr5:92924800-92925600	Active TSS	Fetal Brain Male	brain
28	chr5:92924800-92925800	Weak transcription	Right Atrium	heart
29	chr5:92924800-92926400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr5:92924800-92929400	Weak transcription	Osteobl	bone
31	chr5:92925000-92926000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:92925000-92926200	Flanking Active TSS	NH-A	brain
33	chr5:92925000-92926800	Strong transcription	HSMM	muscle
34	chr5:92925200-92925600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:92925200-92926200	Genic enhancers	Hela-S3	cervix
36	chr5:92925200-92927200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:92925200-92927200	Active TSS	Brain Hippocampus Middle	brain
38	chr5:92925200-92927400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:92925200-92928800	Weak transcription	Brain Substantia Nigra	brain
40	chr5:92925400-92925600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:92925400-92925600	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr5:92925400-92925600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
43	chr5:92925400-92926000	Genic enhancers	Ovary	ovary
44	chr5:92925400-92926200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:92925400-92927600	Genic enhancers	HepG2	liver

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