Variant report

Variant	rs449074
Chromosome Location	chr6:28539308-28539309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28532530..28535314-chr6:28537966..28540071,2	K562	blood:
2	chr6:28536151..28541638-chr6:28552777..28557302,5	MCF-7	breast:
3	chr6:28508315..28510538-chr6:28538499..28540306,2	K562	blood:
4	chr6:28529471..28535442-chr6:28536902..28541186,7	K562	blood:
5	chr6:28537910..28539578-chr6:28542732..28545368,2	MCF-7	breast:
6	chr6:28530142..28532374-chr6:28538545..28540878,2	K562	blood:

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction
ENSG00000246350	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10080420	0.81[ASN][1000 genomes]
rs10434846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733177	1.00[ASN][1000 genomes]
rs10755647	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807036	0.83[ASN][1000 genomes]
rs10807040	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758055	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332986	0.81[ASN][1000 genomes]
rs1474986	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2057295	1.00[ASN][1000 genomes]
rs2108924	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2191036	0.81[ASN][1000 genomes]
rs2394119	1.00[ASN][1000 genomes]
rs28382606	1.00[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs34358978	0.93[ASN][1000 genomes]
rs34931542	0.93[ASN][1000 genomes]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs381493	1.00[ASN][1000 genomes]
rs384399	1.00[ASN][1000 genomes]
rs3852211	1.00[ASN][1000 genomes]
rs389603	1.00[ASN][1000 genomes]
rs392471	0.88[ASN][1000 genomes]
rs394772	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399558	0.97[ASN][1000 genomes]
rs3999023	1.00[ASN][1000 genomes]
rs402426	1.00[ASN][1000 genomes]
rs404343	1.00[ASN][1000 genomes]
rs408255	1.00[ASN][1000 genomes]
rs411538	1.00[ASN][1000 genomes]
rs4121090	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418628	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418898	1.00[ASN][1000 genomes]
rs420436	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420463	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422089	0.97[ASN][1000 genomes]
rs424426	1.00[ASN][1000 genomes]
rs426922	1.00[ASN][1000 genomes]
rs429875	1.00[ASN][1000 genomes]
rs434636	1.00[ASN][1000 genomes]
rs442174	0.90[ASN][1000 genomes]
rs443924	1.00[ASN][1000 genomes]
rs454746	1.00[ASN][1000 genomes]
rs4711176	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713172	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713174	1.00[ASN][1000 genomes]
rs5007575	0.94[ASN][1000 genomes]
rs55860825	1.00[ASN][1000 genomes]
rs6456820	0.81[ASN][1000 genomes]
rs6456829	1.00[ASN][1000 genomes]
rs6456832	1.00[ASN][1000 genomes]
rs6456833	1.00[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6906826	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6923163	1.00[ASN][1000 genomes]
rs6925972	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6935589	0.93[ASN][1000 genomes]
rs6937042	0.93[ASN][1000 genomes]
rs6938371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6941222	0.81[ASN][1000 genomes]
rs7381746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7382309	1.00[ASN][1000 genomes]
rs7382583	1.00[ASN][1000 genomes]
rs7761914	1.00[ASN][1000 genomes]
rs7771490	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773193	1.00[ASN][1000 genomes]
rs911177	1.00[ASN][1000 genomes]
rs911178	0.88[ASN][1000 genomes]
rs9393922	1.00[ASN][1000 genomes]
rs9393923	1.00[ASN][1000 genomes]
rs9461457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9461464	0.93[ASN][1000 genomes]
rs9468384	0.81[ASN][1000 genomes]
rs9468394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28531800-28553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28532000-28552600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:28534400-28543200	Weak transcription	Liver	Liver
4	chr6:28535000-28554000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:28536600-28553200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:28536800-28540000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:28537200-28540800	Weak transcription	Fetal Brain Female	brain
8	chr6:28537200-28542200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:28537200-28543800	Weak transcription	GM12878-XiMat	blood
10	chr6:28537200-28553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28537400-28541600	Weak transcription	K562	blood
13	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:28537600-28540600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:28537800-28541200	Weak transcription	Brain Germinal Matrix	brain
16	chr6:28538800-28553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:28539000-28541200	Weak transcription	A549	lung

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