Variant report

Variant	rs2221335
Chromosome Location	chr6:54737431-54737432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54587916..54591176-chr6:54736715..54740306,4	MCF-7	breast:
2	chr6:54736804..54741584-chr6:54742863..54746409,5	MCF-7	breast:
3	chr6:54704497..54716767-chr6:54728797..54750947,71	MCF-7	breast:
4	chr6:54572095..54573836-chr6:54736894..54738679,2	MCF-7	breast:
5	chr6:54562484..54564963-chr6:54735331..54738094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000224984	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1155748	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1503138	0.97[EUR][1000 genomes]
rs1503153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1503155	0.83[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17678648	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs239784	0.83[CEU][hapmap];0.95[YRI][hapmap]
rs239786	1.00[CEU][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239795	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239800	0.87[EUR][1000 genomes]
rs239804	0.87[EUR][1000 genomes]
rs239809	0.87[EUR][1000 genomes]
rs239811	0.87[EUR][1000 genomes]
rs239814	0.82[EUR][1000 genomes]
rs239817	0.82[EUR][1000 genomes]
rs239820	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs239821	0.87[EUR][1000 genomes]
rs239822	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2746441	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2746442	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3125262	0.80[EUR][1000 genomes]
rs3135456	0.80[EUR][1000 genomes]
rs376894	0.87[EUR][1000 genomes]
rs4143677	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715488	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6459030	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs7749067	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761633	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs869859	0.80[EUR][1000 genomes]
rs905460	0.80[EUR][1000 genomes]
rs9357820	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9367595	0.92[EUR][1000 genomes]
rs9396004	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs973206	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980820	0.80[EUR][1000 genomes]
rs995852	1.00[CEU][hapmap];0.97[EUR][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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54725600-54737600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:54726600-54739600	Weak transcription	Small Intestine	intestine
3	chr6:54727200-54748800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:54727400-54740400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:54727400-54743800	Weak transcription	Pancreas	Pancrea
6	chr6:54730400-54743800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:54731600-54739400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:54731800-54738800	Weak transcription	Fetal Intestine Large	intestine
9	chr6:54731800-54738800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:54732200-54739200	Weak transcription	Fetal Intestine Small	intestine
11	chr6:54734600-54741800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:54735000-54738200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:54736600-54737800	Genic enhancers	NHEK	skin
14	chr6:54736800-54741800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:54737200-54737600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:54737200-54737600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:54737200-54738000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:54737200-54742200	Enhancers	HMEC	breast
19	chr6:54737200-54746400	Enhancers	Hela-S3	cervix
20	chr6:54737400-54737600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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