Variant report

Variant	rs662202
Chromosome Location	chr19:39536703-39536704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39521423..39523663-chr19:39535001..39537936,2	MCF-7	breast:
2	chr19:39536592..39538414-chr19:39541757..39543284,2	MCF-7	breast:
3	chr19:39528736..39531074-chr19:39534796..39537090,2	K562	blood:
4	chr19:39521025..39525658-chr19:39535006..39538345,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267992	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10409280	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10411234	0.91[ASN][1000 genomes]
rs10411271	0.83[ASN][1000 genomes]
rs12463075	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12609401	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12609806	0.83[LWK][hapmap]
rs12974080	0.90[ASN][1000 genomes]
rs12974708	0.82[ASN][1000 genomes]
rs12975482	0.84[ASN][1000 genomes]
rs12976100	0.82[ASN][1000 genomes]
rs12979968	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981133	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12981826	0.82[EUR][1000 genomes]
rs12982067	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12983352	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12984833	0.82[ASN][1000 genomes]
rs12984836	0.82[ASN][1000 genomes]
rs13345897	0.85[ASN][1000 genomes]
rs1626050	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1627631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628426	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1629253	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1651747	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654336	0.80[CHB][hapmap]
rs16973058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17795157	0.80[CHB][hapmap]
rs1864186	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864188	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1869982	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2318897	0.85[ASN][1000 genomes]
rs2562330	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs34240661	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34366439	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35000840	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35622111	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35940388	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802010	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs482342	0.80[CHB][hapmap]
rs483359	0.80[CHB][hapmap]
rs487356	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498586	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs500691	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs516901	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523890	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs523943	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553330	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554932	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561148	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561329	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564474	0.80[CHB][hapmap]
rs572764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57401831	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57724551	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs582575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584822	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586107	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586176	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59698424	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs598468	0.96[ASN][1000 genomes]
rs599230	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602899	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61553368	0.93[ASN][1000 genomes]
rs618068	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119464	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62119508	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62119510	0.93[ASN][1000 genomes]
rs62121530	0.80[EUR][1000 genomes]
rs62121532	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs678772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678848	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678885	0.80[CHB][hapmap]
rs679657	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679732	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246076	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs930100	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv526711	chr19:39533754-39538592	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv458570	chr19:39533754-39538592	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv579507	chr19:39533754-39538592	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs662202	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs662202	BLOC1S3	cis	cerebellum	SCAN
rs662202	C19orf61	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39530800-39543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr19:39535400-39538800	Enhancers	Fetal Intestine Large	intestine
3	chr19:39535400-39538800	Enhancers	Fetal Intestine Small	intestine
4	chr19:39535800-39538800	Enhancers	Duodenum Mucosa	Duodenum
5	chr19:39536400-39536800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr19:39536400-39536800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:39536400-39536800	Flanking Bivalent TSS/Enh	HepG2	liver
8	chr19:39536400-39537200	Enhancers	Placenta	Placenta
9	chr19:39536400-39537200	Enhancers	Hela-S3	cervix
10	chr19:39536400-39537400	Flanking Active TSS	K562	blood
11	chr19:39536400-39538200	Enhancers	Stomach Mucosa	stomach
12	chr19:39536600-39536800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:39536600-39537000	Flanking Active TSS	A549	lung
14	chr19:39536600-39537400	Enhancers	GM12878-XiMat	blood
15	chr19:39536600-39537600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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