Variant report

Variant	rs410663
Chromosome Location	chr8:90871689-90871690
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90869811..90872309-chr8:90877173..90879191,2	MCF-7	breast:
2	chr8:90871125..90874218-chr8:90995397..90997116,3	MCF-7	breast:
3	chr8:90867270..90880457-chr8:90913050..90918593,18	MCF-7	breast:
4	chr8:90864006..90868898-chr8:90869518..90873802,5	K562	blood:
5	chr8:90869160..90871090-chr8:90871381..90873801,2	MCF-7	breast:
6	chr8:90869094..90872518-chr8:90873810..90876034,4	MCF-7	breast:
7	chr8:90864006..90868898-chr8:90869518..90873896,4	K562	blood:
8	chr8:90868769..90874649-chr8:90891359..90894975,5	MCF-7	breast:
9	chr8:90866711..90872793-chr8:90887380..90891820,9	MCF-7	breast:
10	chr8:90858582..90866507-chr8:90866541..90873248,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104320	Chromatin interaction
ENSG00000207359	Chromatin interaction
ENSG00000164823	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1003843	0.81[CEU][hapmap]
rs10112852	0.81[CEU][hapmap]
rs12675822	0.84[ASN][1000 genomes]
rs12679902	0.84[ASN][1000 genomes]
rs12680009	0.84[ASN][1000 genomes]
rs13277948	0.84[ASN][1000 genomes]
rs218902	0.81[CEU][hapmap]
rs2189025	0.83[ASN][1000 genomes]
rs218907	0.81[CEU][hapmap]
rs218908	0.81[CEU][hapmap]
rs218913	0.81[CEU][hapmap]
rs218929	0.81[CEU][hapmap]
rs365871	0.95[AFR][1000 genomes]
rs366867	0.94[ASN][1000 genomes]
rs367640	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs370282	0.86[JPT][hapmap]
rs374957	0.92[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs376962	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs377897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs379015	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380425	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs381456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs386587	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs386857	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs388866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs390536	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs39499	0.81[CEU][hapmap]
rs39500	0.81[CEU][hapmap]
rs39506	0.81[CEU][hapmap]
rs39519	0.92[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs39761	0.81[CEU][hapmap]
rs39771	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs39772	0.92[EUR][1000 genomes]
rs398959	0.88[AFR][1000 genomes]
rs400571	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs40250	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs402886	0.81[CEU][hapmap]
rs40452	0.81[CEU][hapmap]
rs40459	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40547	0.86[JPT][hapmap]
rs40638	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs410577	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs418634	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419890	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs42186	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs42346	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs42481	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42490	0.81[CEU][hapmap]
rs425140	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs425312	0.92[EUR][1000 genomes]
rs426240	0.92[EUR][1000 genomes]
rs427854	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs43134	0.81[CEU][hapmap]
rs43136	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs43225	0.81[CEU][hapmap]
rs43229	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs432457	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs438485	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs447618	0.81[CEU][hapmap]
rs447989	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs410663	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs410663	MMP16	cis	cerebellum	SCAN
rs410663	OSGIN2	cis	parietal	SCAN
rs410663	RIPK2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90866600-90873400	Enhancers	HSMMtube	muscle
2	chr8:90868200-90872000	Enhancers	HSMM	muscle
3	chr8:90869000-90872000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:90869200-90873800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr8:90869600-90872400	Enhancers	Adipose Nuclei	Adipose
6	chr8:90869800-90872400	Enhancers	Rectal Smooth Muscle	rectum
7	chr8:90870000-90874200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:90870200-90871800	Enhancers	Colon Smooth Muscle	Colon
9	chr8:90871000-90874400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr8:90871200-90872200	Enhancers	A549	lung
11	chr8:90871200-90872800	Weak transcription	Fetal Muscle Leg	muscle
12	chr8:90871200-90873800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr8:90871400-90871800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:90871600-90874200	Weak transcription	Brain Substantia Nigra	brain

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