Variant report

Variant	rs4392657
Chromosome Location	chr5:118358569-118358570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:118357201..118359972-chr5:118405871..118408203,2	MCF-7	breast:
2	chr5:118357582..118358760-chr5:118747481..118748200,3	MCF-7	breast:
3	chr5:118356332..118359280-chr5:118404469..118406379,2	K562	blood:
4	chr5:118357160..118359907-chr5:118603560..118606226,2	MCF-7	breast:
5	chr5:118322908..118325429-chr5:118357118..118359882,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction
ENSG00000239011	Chromatin interaction
ENSG00000249494	Chromatin interaction
ENSG00000172869	Chromatin interaction
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10519564	1.00[CHB][hapmap]
rs11959589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12109156	1.00[CHB][hapmap]
rs12109252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1448479	1.00[JPT][hapmap]
rs1510971	1.00[CHB][hapmap]
rs17132677	1.00[CHB][hapmap]
rs17144714	1.00[JPT][hapmap]
rs17144824	1.00[CHB][hapmap]
rs17144836	1.00[CHB][hapmap]
rs17144872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144883	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17144893	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17381247	1.00[JPT][hapmap]
rs17440213	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2029036	1.00[JPT][hapmap]
rs2084460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2115301	1.00[JPT][hapmap]
rs2217310	1.00[CHB][hapmap]
rs2377127	1.00[CHB][hapmap]
rs299218	0.85[EUR][1000 genomes]
rs34671950	0.92[ASN][1000 genomes]
rs3813297	1.00[JPT][hapmap]
rs3813298	1.00[JPT][hapmap]
rs4634381	1.00[CHB][hapmap]
rs4895184	1.00[JPT][hapmap]
rs4895353	1.00[JPT][hapmap]
rs4895354	1.00[JPT][hapmap]
rs55741500	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55805551	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56664193	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860946	1.00[CHB][hapmap]
rs6862297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6863802	1.00[CHB][hapmap]
rs6870923	1.00[CHB][hapmap]
rs6874399	1.00[CHB][hapmap]
rs6880144	1.00[CHB][hapmap]
rs6892437	1.00[CHB][hapmap]
rs72784039	0.82[ASN][1000 genomes]
rs7706037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7710339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7723221	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7724403	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7724753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7734815	1.00[CHB][hapmap]
rs7737716	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1018539	chr5:118355284-118445244	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118350600-118360000	Enhancers	Primary B cells from peripheral blood	blood
2	chr5:118351600-118359800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:118353400-118358600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:118355200-118367600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:118355600-118360000	Enhancers	Primary B cells from cord blood	blood
6	chr5:118356000-118359600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr5:118356200-118359200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:118357800-118359400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr5:118357800-118359600	Enhancers	Stomach Mucosa	stomach
10	chr5:118357800-118359600	Enhancers	GM12878-XiMat	blood
11	chr5:118358000-118358600	Enhancers	Fetal Thymus	thymus
12	chr5:118358000-118359200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:118358200-118358600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr5:118358200-118359200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:118358400-118358600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:118358400-118359000	Weak transcription	Thymus	Thymus

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