Variant report

Variant	rs11669258
Chromosome Location	chr19:35724000-35724001
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:35720837..35725765-chr19:35738586..35741342,4	K562	blood:
2	chr19:35723373..35727135-chr19:35736732..35741150,5	MCF-7	breast:
3	chr19:35719219..35721551-chr19:35722834..35727069,3	K562	blood:

Variant related genes	Relation type
ENSG00000177558	Chromatin interaction
ENSG00000105699	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10407740	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10411872	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10412357	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10416254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421791	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10422195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084809	0.96[CEU][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12609790	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073900	0.82[JPT][hapmap]
rs2188327	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2861485	0.96[CEU][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2861487	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2861488	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34926220	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4805118	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4806117	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4806119	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4806122	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4806123	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56209605	0.94[EUR][1000 genomes]
rs6510474	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248460	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249852	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7249941	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7249962	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7250531	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7251826	0.85[ASW][hapmap];0.83[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7253876	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7255786	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7256604	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73029964	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73029965	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73029970	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7359971	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs8112032	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv2763203	chr19:35700047-35738400	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	nsv9710	chr19:35720181-35724894	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv524195	chr19:35722226-35724000	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11669258	CD177	cis	parietal	SCAN
rs11669258	FCGBP	cis	cerebellum	SCAN
rs11669258	ZNF383	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35716400-35724400	Weak transcription	Lung	lung
2	chr19:35723000-35724000	Enhancers	H9 Cell Line	embryonic stem cell
3	chr19:35723600-35724200	Enhancers	HepG2	liver
4	chr19:35723800-35724400	Enhancers	Fetal Intestine Small	intestine
5	chr19:35723800-35725800	Weak transcription	Spleen	Spleen

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