Variant report

Variant	rs28705201
Chromosome Location	chr4:99168006-99168007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99166826..99169265-chr4:99180288..99182314,2	MCF-7	breast:
2	chr4:99166387..99172078-chr4:99179541..99183519,6	K562	blood:
3	chr4:99167094..99174507-chr4:99179352..99184320,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138698	Chromatin interaction
ENSG00000214559	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10001137	0.80[AMR][1000 genomes]
rs10003061	0.80[AMR][1000 genomes]
rs10003496	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10006734	0.80[AMR][1000 genomes]
rs10010260	0.80[AMR][1000 genomes]
rs10013248	0.80[AMR][1000 genomes]
rs10015953	0.80[AMR][1000 genomes]
rs10017075	0.80[AMR][1000 genomes]
rs10017827	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10022073	0.80[AMR][1000 genomes]
rs10025311	0.80[AMR][1000 genomes]
rs10026222	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10027925	0.80[AMR][1000 genomes]
rs10029895	0.80[AMR][1000 genomes]
rs10034649	0.80[AMR][1000 genomes]
rs10212883	0.80[AMR][1000 genomes]
rs10470953	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13353633	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17027388	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17027393	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17027526	0.80[AMR][1000 genomes]
rs17027538	0.80[AMR][1000 genomes]
rs28407050	0.80[AMR][1000 genomes]
rs28438716	0.80[AMR][1000 genomes]
rs28446845	0.80[AMR][1000 genomes]
rs28455818	0.80[AMR][1000 genomes]
rs28472340	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28478192	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28494643	0.80[AMR][1000 genomes]
rs28529663	0.80[AMR][1000 genomes]
rs28558542	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28564255	0.80[AMR][1000 genomes]
rs28589745	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28647503	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28651612	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28664868	0.80[AMR][1000 genomes]
rs28731135	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28786730	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28806635	0.80[AMR][1000 genomes]
rs28807427	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28840158	0.80[AMR][1000 genomes]
rs28893208	0.80[AMR][1000 genomes]
rs41275693	0.80[AMR][1000 genomes]
rs41525749	0.80[AMR][1000 genomes]
rs56805018	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs59725407	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6831386	0.80[AMR][1000 genomes]
rs6834495	0.80[AMR][1000 genomes]
rs6858042	0.80[AMR][1000 genomes]
rs73832156	0.91[AFR][1000 genomes]
rs73834403	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73834404	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73834429	0.80[AMR][1000 genomes]
rs73834444	0.80[AMR][1000 genomes]
rs73834479	0.80[AMR][1000 genomes]
rs7655622	0.84[AFR][1000 genomes]
rs7656868	0.80[AMR][1000 genomes]
rs7658383	0.80[AMR][1000 genomes]
rs9991668	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9993166	0.83[AMR][1000 genomes]
rs9994467	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1000956	chr4:98732458-99178588	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv879650	chr4:99057457-99172232	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv461595	chr4:99065480-99172175	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv594939	chr4:99065480-99172175	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99164400-99180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:99167800-99168400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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