Variant report

Variant	rs9371228
Chromosome Location	chr6:150243113-150243114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150182735..150186007-chr6:150239527..150243180,4	MCF-7	breast:
2	chr6:149865589..149867401-chr6:150242514..150245357,2	MCF-7	breast:
3	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000131013	Chromatin interaction
ENSG00000164520	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10457852	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12204653	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12209310	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210822	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12527391	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12528243	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1855572	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1999632	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1999633	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2342766	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3798763	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3922946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3922947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473864	0.92[ASN][1000 genomes]
rs4869755	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869756	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869767	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869768	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870078	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4870110	0.92[ASN][1000 genomes]
rs4870117	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4870118	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5024811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57894361	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6557165	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6912330	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914185	0.83[ASN][1000 genomes]
rs6925151	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7452592	0.83[EUR][1000 genomes]
rs7764677	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs915140	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322229	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9383941	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9397070	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970172	chr6:150235248-150244455	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9371228	RP11-350J20.5	cis	lung	GTEx
rs9371228	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9371228	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9371228	RAET1G	cis	Thyroid	GTEx
rs9371228	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9371228	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150227800-150243400	Weak transcription	Right Ventricle	heart
2	chr6:150230400-150243600	Weak transcription	Pancreas	Pancrea
3	chr6:150237200-150243600	Weak transcription	Right Atrium	heart
4	chr6:150239400-150243200	Weak transcription	HMEC	breast
5	chr6:150239600-150243400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:150239600-150243400	Weak transcription	NHEK	skin
7	chr6:150239800-150243400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:150239800-150243400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:150239800-150243600	Weak transcription	Esophagus	oesophagus
10	chr6:150241200-150243800	Weak transcription	Aorta	Aorta
11	chr6:150242400-150243800	Enhancers	Spleen	Spleen
12	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:150243000-150243400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:150243000-150243800	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr6:150243000-150243800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links