Variant report

Variant	rs10804692
Chromosome Location	chr3:143062327-143062328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143061262..143062878-chr3:143065854..143067728,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST2-3	chr3:143062192-143062456	ENSG00000240012.1

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11711068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11716489	1.00[JPT][hapmap]
rs11717437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11718728	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11915421	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11915761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11927016	1.00[CHB][hapmap]
rs13061014	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13074801	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1501624	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1501631	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604377	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1604380	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1609727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610217	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16853767	1.00[CHB][hapmap]
rs17637392	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs1812200	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1995356	1.00[CHB][hapmap]
rs35842913	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839627	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7627844	1.00[CHB][hapmap]
rs7642361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs7652557	1.00[CHB][hapmap]
rs894176	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs9850863	1.00[CHB][hapmap]
rs9862119	1.00[CHB][hapmap]

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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv877564	chr3:143059952-143116883	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10804692	PLSCR1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143056800-143062400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143060200-143062600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:143061200-143062400	Enhancers	Fetal Thymus	thymus
4	chr3:143061400-143063600	Enhancers	HUVEC	blood vessel
5	chr3:143061400-143064000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:143061600-143064200	Enhancers	Dnd41	blood
7	chr3:143061800-143062600	Enhancers	Brain Angular Gyrus	brain
8	chr3:143061800-143066800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:143062000-143062400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:143062200-143063800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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