Variant report

Variant	rs6459034
Chromosome Location	chr6:54748681-54748682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54564646..54566812-chr6:54747166..54750251,3	MCF-7	breast:
2	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224984	Chromatin interaction
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	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs10948866	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs10948879	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192659	0.87[CHB][hapmap]
rs12208341	0.83[AMR][1000 genomes]
rs12208348	0.83[AMR][1000 genomes]
rs12211168	0.82[AMR][1000 genomes]
rs1393776	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1472679	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs148109	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs171224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs181155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963697	0.93[CHB][hapmap]
rs2134539	0.85[EUR][1000 genomes]
rs2179786	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2207025	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2207026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239779	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239792	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239794	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs239796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239801	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239813	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs239815	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs239837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs239850	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239854	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2746443	0.82[EUR][1000 genomes]
rs2816810	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2816811	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2816812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996950	0.80[EUR][1000 genomes]
rs421957	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs4712082	0.86[CHB][hapmap]
rs6918402	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs6926997	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6937970	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs7741915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7765721	0.84[CEU][hapmap];0.93[CHB][hapmap]
rs931766	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs9349740	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9370345	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9382403	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs971526	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs973205	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs988913	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[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	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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54727200-54748800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:54737600-54755800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
4	chr6:54743000-54752000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:54744200-54757600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:54744800-54751400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:54744800-54752000	Weak transcription	Fetal Intestine Large	intestine
9	chr6:54744800-54755800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:54746200-54753400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:54746200-54755200	Weak transcription	NHEK	skin
12	chr6:54746200-54755600	Weak transcription	HMEC	breast
13	chr6:54746400-54757800	Weak transcription	Hela-S3	cervix
14	chr6:54747600-54756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:54748600-54749200	Strong transcription	Fetal Intestine Small	intestine

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