Variant report

Variant	rs10499669
Chromosome Location	chr7:48022274-48022275
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	CTCF	chr7:48022240-48022390	AG10803	skin:	n/a	n/a
2	POLR2A	chr7:48022028-48022763	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:48022165-48022690	H1-neurons	neurons:	n/a	n/a
4	EBF1	chr7:48022180-48022586	GM12878	blood:	n/a	chr7:48022439-48022449 chr7:48022378-48022387 chr7:48022376-48022389 chr7:48022377-48022388 chr7:48022439-48022448

Variant related genes	Relation type
HUS1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10261436	0.88[EUR][1000 genomes]
rs12667562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669119	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17131948	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2307252	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2348665	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686782	0.86[YRI][hapmap]
rs2686792	0.81[YRI][hapmap]
rs3176491	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176568	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176581	0.91[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3176595	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36213466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4720625	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56075223	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59023024	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59920101	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62447088	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62447089	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62447093	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73695940	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs885338	0.91[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10499669	PKD1L1	cis	cerebellum	SCAN
rs10499669	PKD1L1	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48019400-48028800	Weak transcription	Fetal Lung	lung
2	chr7:48019800-48028200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:48019800-48031600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:48020800-48023600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:48021600-48022400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:48022000-48022600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr7:48022000-48022600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr7:48022000-48022600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:48022000-48022600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:48022000-48022600	Enhancers	NHDF-Ad	bronchial
11	chr7:48022000-48022800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:48022000-48023200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:48022200-48022400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr7:48022200-48022400	Enhancers	A549	lung
15	chr7:48022200-48022600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr7:48022200-48022600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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