Variant report

Variant	rs16886073
Chromosome Location	chr6:54729255-54729256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:
2	chr6:54718981..54722041-chr6:54724023..54729682,8	MCF-7	breast:
3	chr6:54583583..54586469-chr6:54727325..54729845,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1155750	1.00[ASN][1000 genomes]
rs1503137	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1503150	1.00[CHB][hapmap]
rs16886072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886088	1.00[CEU][hapmap];1.00[CHB][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]
rs16886105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239787	1.00[CHB][hapmap]
rs239788	1.00[CHB][hapmap]
rs239789	1.00[CHB][hapmap]
rs239791	1.00[CHB][hapmap]
rs239793	1.00[CHB][hapmap]
rs239798	1.00[CHB][hapmap]
rs239802	1.00[CHB][hapmap]
rs239805	1.00[CHB][hapmap]
rs239823	1.00[CHB][hapmap]
rs239824	1.00[CHB][hapmap]
rs239828	1.00[CHB][hapmap]
rs239829	1.00[CHB][hapmap]
rs239830	1.00[CHB][hapmap]
rs239831	1.00[CHB][hapmap]
rs239832	1.00[CHB][hapmap]
rs239833	1.00[CHB][hapmap]
rs239834	1.00[CHB][hapmap]
rs239836	1.00[CHB][hapmap]
rs239838	1.00[CHB][hapmap]
rs239839	1.00[CHB][hapmap]
rs239840	1.00[CHB][hapmap]
rs239841	1.00[CHB][hapmap]
rs239843	1.00[CHB][hapmap]
rs239846	1.00[CHB][hapmap]
rs239847	1.00[CHB][hapmap]
rs239848	1.00[CHB][hapmap]
rs239852	1.00[CHB][hapmap]
rs239853	1.00[CHB][hapmap]
rs2746440	1.00[CHB][hapmap]
rs398483	1.00[CHB][hapmap]
rs406149	1.00[CHB][hapmap]
rs41431945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56745332	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56804573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57271459	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437775	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73437777	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73437783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73437796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73439703	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73439709	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7453441	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7739951	1.00[CEU][hapmap];1.00[CHB][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]
rs7743188	1.00[CHB][hapmap]
rs7773204	1.00[CHB][hapmap]
rs9349735	1.00[CHB][hapmap]
rs9367588	1.00[CHB][hapmap]
rs9367589	1.00[CHB][hapmap]
rs9367596	1.00[CHB][hapmap]
rs9370335	1.00[CHB][hapmap]
rs9382377	1.00[CHB][hapmap]
rs9382388	1.00[CHB][hapmap]
rs9395992	1.00[CHB][hapmap]
rs9475077	1.00[CHB][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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54715400-54731200	Weak transcription	Hela-S3	cervix
2	chr6:54721200-54730000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:54725400-54731400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:54725600-54729800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:54725600-54737400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:54725600-54737600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:54725800-54730000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:54725800-54730000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:54725800-54730000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:54726600-54739600	Weak transcription	Small Intestine	intestine
11	chr6:54727000-54730000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:54727000-54730600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:54727200-54729800	Weak transcription	Stomach Mucosa	stomach
14	chr6:54727200-54730000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:54727200-54731400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:54727200-54732800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:54727200-54748800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:54727400-54730000	Weak transcription	Fetal Kidney	kidney
19	chr6:54727400-54740400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:54727400-54743800	Weak transcription	Pancreas	Pancrea
21	chr6:54728400-54729800	Weak transcription	Fetal Intestine Small	intestine
22	chr6:54728600-54732800	Weak transcription	NHEK	skin
23	chr6:54729000-54729400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:54729000-54731800	Enhancers	Fetal Heart	heart
25	chr6:54729200-54729400	Enhancers	Fetal Intestine Large	intestine
26	chr6:54729200-54729400	Enhancers	Gastric	stomach
27	chr6:54729200-54733400	Weak transcription	HMEC	breast

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