Variant report

Variant	rs6005923
Chromosome Location	chr22:29252365-29252366
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29193593..29195791-chr22:29251610..29254228,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12330071	0.86[EUR][1000 genomes]
rs16987090	0.81[JPT][hapmap]
rs17880353	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs17880459	0.85[YRI][hapmap]
rs17881056	0.85[YRI][hapmap]
rs17884212	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs2206061	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2228260	0.86[EUR][1000 genomes]
rs2235432	0.91[JPT][hapmap]
rs41281603	0.86[EUR][1000 genomes]
rs41382448	0.81[JPT][hapmap]
rs5752839	1.00[MEX][hapmap]
rs5762814	0.85[YRI][hapmap]
rs5762893	1.00[MEX][hapmap]
rs5762900	1.00[MEX][hapmap]
rs5762906	1.00[MEX][hapmap]
rs5997401	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6005861	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs6005868	0.91[JPT][hapmap]
rs6005870	0.86[EUR][1000 genomes]
rs6005874	0.86[EUR][1000 genomes]
rs6005898	0.86[EUR][1000 genomes]
rs6005899	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6005924	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288513	1.00[MEX][hapmap]
rs7290364	1.00[MEX][hapmap]
rs9625551	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs9625565	0.86[EUR][1000 genomes]
rs9625575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9625580	0.86[EUR][1000 genomes]
rs9625645	1.00[MEX][hapmap]
rs9625657	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 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	chr22:29251200-29252400	Enhancers	Duodenum Mucosa	Duodenum
2	chr22:29251200-29252400	Enhancers	Fetal Intestine Large	intestine
3	chr22:29251400-29252400	Enhancers	Fetal Intestine Small	intestine
4	chr22:29251400-29253600	Enhancers	HepG2	liver
5	chr22:29251600-29252400	Enhancers	Liver	Liver
6	chr22:29251600-29252400	Enhancers	HMEC	breast
7	chr22:29251800-29252400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr22:29252000-29252400	Weak transcription	Pancreas	Pancrea
9	chr22:29252000-29253000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr22:29252000-29253000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr22:29252200-29253200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr22:29252200-29253400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links