Variant report

Variant	rs10052229
Chromosome Location	chr5:127260648-127260649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:127259102..127261566-chr5:127419216..127421910,4	MCF-7	breast:
2	chr5:127257196..127261867-chr5:127264373..127267767,5	MCF-7	breast:
3	chr5:127257978..127262943-chr5:127415784..127421768,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10477678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173229	0.81[ASN][1000 genomes]
rs12173231	0.81[ASN][1000 genomes]
rs12654649	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520246	0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs17164505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176831	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2263502	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409034	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409035	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2409036	0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2681509	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835933	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4836341	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4836343	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4836345	0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs56806325	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865186	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73331900	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73333517	0.81[ASN][1000 genomes]
rs73333527	0.81[ASN][1000 genomes]
rs7711172	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327457	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr5:127253000-127266200	Weak transcription	Fetal Heart	heart
2	chr5:127253800-127261400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:127258200-127262200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:127258400-127266400	Weak transcription	Gastric	stomach
5	chr5:127258400-127266400	Weak transcription	Pancreas	Pancrea
6	chr5:127259400-127261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:127259400-127261800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:127259400-127262400	Enhancers	A549	lung
9	chr5:127259600-127260800	Enhancers	Stomach Mucosa	stomach
10	chr5:127260000-127261200	Enhancers	HSMMtube	muscle
11	chr5:127260000-127262400	Weak transcription	GM12878-XiMat	blood
12	chr5:127260400-127261200	Weak transcription	Small Intestine	intestine
13	chr5:127260400-127261400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:127260600-127261000	Weak transcription	HMEC	breast
15	chr5:127260600-127262000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:127260600-127265600	Weak transcription	HUVEC	blood vessel

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