Variant report

Variant	rs12498440
Chromosome Location	chr4:99100433-99100434
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99092058..99095008-chr4:99098244..99101009,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200658	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10002767	1.00[JPT][hapmap]
rs10003517	1.00[JPT][hapmap]
rs10005811	1.00[JPT][hapmap]
rs10006820	1.00[JPT][hapmap]
rs10022047	1.00[JPT][hapmap]
rs10028275	1.00[JPT][hapmap]
rs10028373	1.00[JPT][hapmap]
rs10470895	1.00[JPT][hapmap]
rs10470952	1.00[JPT][hapmap]
rs10516429	1.00[JPT][hapmap]
rs12498745	1.00[JPT][hapmap]
rs12499136	1.00[JPT][hapmap]
rs12499530	1.00[JPT][hapmap]
rs12500412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500455	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12501974	1.00[JPT][hapmap]
rs12502398	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503806	1.00[JPT][hapmap]
rs12504523	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12505411	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507425	1.00[JPT][hapmap]
rs12507859	1.00[JPT][hapmap]
rs12508039	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12508445	1.00[JPT][hapmap]
rs12509125	1.00[JPT][hapmap]
rs12509417	1.00[JPT][hapmap]
rs12509809	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510055	1.00[JPT][hapmap]
rs13353584	1.00[JPT][hapmap]
rs1453344	1.00[JPT][hapmap]
rs1580065	1.00[JPT][hapmap]
rs17027244	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027299	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17027302	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17027449	1.00[JPT][hapmap]
rs17027452	1.00[JPT][hapmap]
rs1869352	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869353	1.00[CHB][hapmap]
rs1869354	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1913489	1.00[JPT][hapmap]
rs1913490	1.00[JPT][hapmap]
rs1921416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2081490	1.00[JPT][hapmap]
rs2194896	1.00[JPT][hapmap]
rs2865995	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2865996	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2865997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3974886	1.00[JPT][hapmap]
rs4321644	1.00[JPT][hapmap]
rs4396996	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4593139	1.00[JPT][hapmap]
rs4699335	1.00[JPT][hapmap]
rs4699607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699610	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699622	1.00[JPT][hapmap]
rs4699623	1.00[JPT][hapmap]
rs6532732	1.00[JPT][hapmap]
rs6822914	1.00[JPT][hapmap]
rs6828936	1.00[JPT][hapmap]
rs6831490	1.00[JPT][hapmap]
rs6831730	1.00[JPT][hapmap]
rs6833504	1.00[JPT][hapmap]
rs6835411	1.00[JPT][hapmap]
rs6846417	1.00[JPT][hapmap]
rs7654497	1.00[JPT][hapmap]
rs7655147	1.00[JPT][hapmap]
rs7683964	1.00[JPT][hapmap]
rs7687685	1.00[JPT][hapmap]
rs7694221	1.00[JPT][hapmap]
rs890207	1.00[JPT][hapmap]
rs919027	1.00[JPT][hapmap]
rs919028	1.00[JPT][hapmap]

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	nsv879648	chr4:98547717-99104879	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1000011	chr4:98562308-99101692	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv998270	chr4:99063275-99120404	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv470061	chr4:99078105-99160699	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99098000-99100800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:99098400-99101400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr4:99099600-99102000	Enhancers	Fetal Lung	lung
4	chr4:99100000-99101400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:99100200-99101600	Enhancers	Fetal Brain Male	brain
6	chr4:99100400-99100600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:99100400-99100600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:99100400-99100600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:99100400-99101000	Enhancers	Fetal Brain Female	brain

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