Variant report

Variant	rs2179786
Chromosome Location	chr6:54753340-54753341
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54711519..54714524-chr6:54749320..54755101,5	MCF-7	breast:
2	chr6:54713425..54714965-chr6:54753003..54756000,2	MCF-7	breast:
3	chr6:54751952..54753804-chr6:54753869..54755428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10456176	0.87[CHB][hapmap]
rs10485136	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs10948866	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1115159	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1155749	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs12192659	0.87[CHB][hapmap]
rs1393776	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1472679	0.86[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs148109	0.80[CHB][hapmap]
rs1503147	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs171224	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs181155	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1963697	1.00[CHB][hapmap]
rs2064432	0.81[CHB][hapmap]
rs2143798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207025	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs2207026	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs239779	0.80[ASN][1000 genomes]
rs239781	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs239783	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs239790	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs239796	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs239801	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs239837	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2816811	0.81[CHB][hapmap]
rs2816812	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4141552	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs4712081	0.81[CHB][hapmap]
rs6459034	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6918402	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6926997	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6937970	0.87[CHB][hapmap]
rs7453866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7741915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7761336	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7765721	0.93[CHB][hapmap]
rs7774660	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs924712	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs9296771	0.81[CHB][hapmap]
rs931766	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs932452	0.81[CHB][hapmap]
rs9349740	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs9367597	0.81[CHB][hapmap]
rs9370337	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9370345	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9382403	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs971526	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs973205	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs988913	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54737600-54755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
3	chr6:54744200-54757600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:54744800-54755800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:54746200-54753400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54746200-54755200	Weak transcription	NHEK	skin
8	chr6:54746200-54755600	Weak transcription	HMEC	breast
9	chr6:54746400-54757800	Weak transcription	Hela-S3	cervix
10	chr6:54747600-54756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:54752200-54759000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:54752400-54758600	Weak transcription	Rectal Mucosa Donor 31	rectum

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