Variant report

Variant	rs28862677
Chromosome Location	chr4:631555-631556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:629516..632051-chr4:640070..643057,2	MCF-7	breast:
2	chr4:514493..516331-chr4:631156..634018,2	K562	blood:

Variant related genes	Relation type
ENSG00000174227	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10001451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10006278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10018607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10020292	1.00[AMR][1000 genomes]
rs10023609	1.00[AMR][1000 genomes]
rs10023934	0.85[AFR][1000 genomes]
rs10024023	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025758	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028537	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10029924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10030020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10035021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12331186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28366852	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28413992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28414606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28436699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28452973	0.87[AFR][1000 genomes]
rs28459140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28477853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28478159	1.00[AMR][1000 genomes]
rs28510278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28510755	1.00[AMR][1000 genomes]
rs28527330	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28531889	1.00[AMR][1000 genomes]
rs28538930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540058	1.00[AMR][1000 genomes]
rs28546458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28551514	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28594284	0.95[AFR][1000 genomes]
rs28599551	0.90[AFR][1000 genomes]
rs28601829	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28605120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28633819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28671384	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28706206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709824	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28754367	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28818828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28843467	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827034	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835327	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6842140	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73056559	1.00[AMR][1000 genomes]
rs7655485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7665160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671294	1.00[AMR][1000 genomes]
rs7680416	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689014	1.00[AMR][1000 genomes]
rs7696942	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9990446	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9991058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9994679	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9995112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9996316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9996400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9999833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	esv1818085	chr4:629099-638615	Bivalent Enhancer Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv1826696	chr4:629099-638615	Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv1834200	chr4:629099-638615	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv593207	chr4:629437-645300	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:626400-642000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:627000-633000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:630000-631600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr4:630400-632000	Enhancers	Fetal Brain Male	brain
5	chr4:630600-631800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr4:630800-632000	Enhancers	Fetal Kidney	kidney
7	chr4:631400-631600	Bivalent Enhancer	Placenta	Placenta
8	chr4:631400-631800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:631400-631800	Active TSS	Brain Hippocampus Middle	brain
10	chr4:631400-631800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr4:631400-632000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:631400-632000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:631400-632000	Active TSS	Fetal Brain Female	brain
14	chr4:631400-657000	Weak transcription	Right Atrium	heart

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