Variant report

Variant	rs9994679
Chromosome Location	chr4:623209-623210
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	chr4:619437..623881-chr4:666212..669300,4	MCF-7	breast:
2	chr4:619501..622132-chr4:622263..626030,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169020	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10001451	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10006278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010598	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015198	0.88[MKK][hapmap];0.82[YRI][hapmap]
rs10017347	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017435	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10018607	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10020292	0.93[MKK][hapmap];1.00[AMR][1000 genomes]
rs10023609	1.00[AMR][1000 genomes]
rs10024023	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10025758	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027392	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028157	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028526	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028537	1.00[AMR][1000 genomes]
rs10029924	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10030020	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10035021	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12331186	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28366852	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399001	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28413992	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28414606	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28436699	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28459140	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28477853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28478159	1.00[AMR][1000 genomes]
rs28510278	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28510755	0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs28527330	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28531889	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs28538930	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540058	1.00[AMR][1000 genomes]
rs28546458	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28551514	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28594284	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs28601829	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28605120	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615478	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28633819	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665728	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28671384	1.00[AMR][1000 genomes]
rs28706206	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709824	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28754367	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28818828	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28843467	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28862677	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34587191	0.82[YRI][hapmap]
rs6827034	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6835327	1.00[AMR][1000 genomes]
rs6842140	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73056559	1.00[AMR][1000 genomes]
rs7655485	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7665160	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671294	0.88[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs7680416	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689014	1.00[AMR][1000 genomes]
rs7696942	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9990446	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9991058	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9995112	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9996316	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9996400	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997898	0.93[MKK][hapmap]
rs9998466	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998594	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998776	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9999833	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	nsv593205	chr4:601791-623629	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	nsv967276	chr4:615881-624526	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
17	esv993737	chr4:618112-628837	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:616800-624200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:619200-624000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:619600-626000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:621800-624000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:622000-624200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr4:623000-625000	Enhancers	Fetal Muscle Leg	muscle
7	chr4:623200-623400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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