Variant report

Variant	rs6050867
Chromosome Location	chr20:25730968-25730969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25730927-25731012	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25722229..25725727-chr20:25729009..25731451,3	MCF-7	breast:
2	chr20:25727469..25729069-chr20:25729208..25731767,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM182B-1	chr20:25730940-25732440	XLOC_013708

Variant related genes	Relation type
ENSG00000226465	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1122769	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12106173	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1343355	0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs1569617	1.00[JPT][hapmap]
rs16987934	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs16988014	1.00[JPT][hapmap]
rs1883528	1.00[JPT][hapmap]
rs2103661	0.85[JPT][hapmap]
rs2387977	0.82[JPT][hapmap]
rs242130	0.81[CHD][hapmap]
rs242133	1.00[JPT][hapmap]
rs3813916	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4113661	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4813579	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4815436	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4815438	0.83[ASW][hapmap];0.80[LWK][hapmap]
rs4815445	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4815450	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6037159	1.00[JPT][hapmap]
rs6037161	1.00[JPT][hapmap]
rs6037164	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6037166	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6037167	1.00[JPT][hapmap]
rs6037169	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6037195	0.82[JPT][hapmap]
rs6037196	1.00[JPT][hapmap]
rs6037199	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6037222	0.82[JPT][hapmap]
rs6037223	1.00[JPT][hapmap]
rs6050710	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050712	1.00[JPT][hapmap]
rs6050717	1.00[JPT][hapmap]
rs6050724	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050725	1.00[JPT][hapmap]
rs6050726	1.00[JPT][hapmap]
rs6050732	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050733	1.00[JPT][hapmap]
rs6050757	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050760	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6050767	1.00[JPT][hapmap]
rs6050770	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050779	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050788	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6050789	1.00[JPT][hapmap]
rs6050791	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6050796	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050799	1.00[JPT][hapmap]
rs6050833	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050840	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6050858	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6083886	1.00[JPT][hapmap]
rs6083896	1.00[JPT][hapmap]
rs6083897	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs6083899	1.00[JPT][hapmap]
rs6115214	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6115215	1.00[JPT][hapmap]
rs6115224	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6115232	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6132848	1.00[JPT][hapmap]
rs6132850	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6138612	1.00[JPT][hapmap]
rs66813885	0.86[ASN][1000 genomes]
rs66983770	0.86[ASN][1000 genomes]
rs7266592	1.00[JPT][hapmap]
rs7269064	0.83[ASN][1000 genomes]
rs8116267	1.00[JPT][hapmap]
rs8120065	1.00[JPT][hapmap]
rs8120594	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs8121648	1.00[JPT][hapmap]
rs926486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs926487	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs928121	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs981441	0.90[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv525033	chr20:25688001-25730968	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
6	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
7	nsv1062442	chr20:25714010-25754838	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6050867	ZNF337	cis	lymphoblastoid	seeQTL
rs6050867	RP4-694B14.5	cis	lung	GTEx
rs6050867	RP4-694B14.5	cis	Thyroid	GTEx
rs6050867	ZNF337	cis	Thyroid	GTEx
rs6050867	ZNF337	cis	Stomach	GTEx
rs6050867	NANP	cis	cerebellum	SCAN
rs6050867	ZNF337	cis	cerebellum	SCAN
rs6050867	CST2	cis	parietal	SCAN
rs6050867	ENTPD6	cis	parietal	SCAN
rs6050867	VSX1	cis	cerebellum	SCAN
rs6050867	NINL	cis	Nerve Tibial	GTEx
rs6050867	ZNF337	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25708000-25731400	Weak transcription	Esophagus	oesophagus
2	chr20:25713400-25731000	Weak transcription	Left Ventricle	heart
3	chr20:25714400-25731200	Weak transcription	Pancreas	Pancrea
4	chr20:25715600-25731400	Weak transcription	Aorta	Aorta
5	chr20:25721000-25731000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:25724400-25731400	Weak transcription	Brain Angular Gyrus	brain
7	chr20:25726000-25731200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:25726000-25731400	Weak transcription	HMEC	breast
9	chr20:25726200-25731200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:25726200-25731200	Weak transcription	NHEK	skin
11	chr20:25727800-25731000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:25728600-25731400	Weak transcription	Gastric	stomach
13	chr20:25728800-25731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:25729000-25731000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:25730600-25731400	Enhancers	Colon Smooth Muscle	Colon
16	chr20:25730600-25732400	Active TSS	Rectal Smooth Muscle	rectum
17	chr20:25730800-25731000	Enhancers	HepG2	liver

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