Variant report

Variant	rs6853480
Chromosome Location	chr4:90059311-90059312
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90031102..90033625-chr4:90058274..90060653,2	MCF-7	breast:
2	chr4:90056532..90059832-chr4:90060213..90062873,3	K562	blood:

Variant related genes	Relation type
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10033484	0.91[JPT][hapmap]
rs11737182	0.91[JPT][hapmap]
rs12640018	0.80[ASN][1000 genomes]
rs13138280	0.86[JPT][hapmap]
rs1398940	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1398944	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458557	0.91[JPT][hapmap]
rs16996143	0.91[JPT][hapmap]
rs17015027	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17015052	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1708668	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1708669	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs1708670	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1795722	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1795727	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1795734	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1795738	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1903007	0.91[JPT][hapmap]
rs1921679	0.86[JPT][hapmap]
rs1921684	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1961979	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2018779	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2085601	0.91[JPT][hapmap]
rs2090031	0.80[ASN][1000 genomes]
rs2178583	0.91[JPT][hapmap]
rs2178584	0.91[JPT][hapmap]
rs2178585	0.91[JPT][hapmap]
rs2609275	0.91[JPT][hapmap]
rs2670623	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2704571	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2704573	0.91[JPT][hapmap]
rs2704577	0.91[JPT][hapmap]
rs28628620	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2869971	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2869972	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2904261	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3927227	0.86[ASN][1000 genomes]
rs4285052	0.83[ASN][1000 genomes]
rs4491985	0.89[ASN][1000 genomes]
rs4507326	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs4642211	0.86[JPT][hapmap]
rs59924504	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60618725	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62306363	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62306364	0.82[ASN][1000 genomes]
rs62306390	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62306391	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62306397	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62306424	0.89[ASN][1000 genomes]
rs6821678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828137	0.89[YRI][hapmap]
rs6844655	0.91[JPT][hapmap]
rs6852373	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs72877642	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs756345	0.89[ASN][1000 genomes]
rs7656238	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7658455	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686954	0.91[JPT][hapmap]
rs7692291	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697075	0.91[JPT][hapmap]
rs7697900	0.91[JPT][hapmap]
rs9307054	0.91[JPT][hapmap]
rs9307055	0.86[JPT][hapmap]
rs9307061	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs9991237	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription 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 target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470052	chr4:90055898-90075384	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv830002	chr4:90056232-90258865	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90056200-90071800	Weak transcription	Right Atrium	heart
2	chr4:90056400-90063400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr4:90057800-90060600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:90059000-90062800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:90059200-90059400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr4:90059200-90064000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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