Variant report

Variant	rs17810802
Chromosome Location	chr11:85390732-85390733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85385043..85387770-chr11:85389067..85391725,3	MCF-7	breast:
2	chr11:85389569..85392078-chr11:85394347..85396779,2	MCF-7	breast:
3	chr11:85376012..85378265-chr11:85390192..85392054,2	K562	blood:
4	chr11:85374551..85377717-chr11:85388541..85395552,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC89-1	chr11:85389665-85393535	NONHSAT023443

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11234386	0.93[ASN][1000 genomes]
rs11234387	0.93[ASN][1000 genomes]
rs11234388	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs11234389	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs11234390	0.88[ASN][1000 genomes]
rs11234391	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11234393	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11234397	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs11607789	0.85[CHB][hapmap]
rs17148355	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs17148514	0.85[CHB][hapmap]
rs17208525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17208602	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17208616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17810701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17810766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17810855	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17811120	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs2044393	1.00[CHB][hapmap]
rs2276018	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs2304342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304343	0.86[JPT][hapmap];1.00[MEX][hapmap]
rs2374638	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs494119	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs56695336	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57431471	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58631677	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59508078	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616309	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs645798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs678376	0.85[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs72953967	0.82[ASN][1000 genomes]
rs72953982	0.86[ASN][1000 genomes]
rs72953991	0.86[ASN][1000 genomes]
rs72953995	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72955904	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72955912	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72955918	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72955922	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72955939	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72958012	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72958014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72958027	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers 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 miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85389000-85393200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:85389200-85392800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:85389400-85392200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:85390000-85392800	Enhancers	Fetal Lung	lung
5	chr11:85390200-85391800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:85390200-85391800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:85390200-85392000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:85390400-85391800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:85390400-85392000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:85390400-85392000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:85390400-85392000	Weak transcription	Ovary	ovary
12	chr11:85390600-85392600	Weak transcription	Fetal Kidney	kidney
13	chr11:85390600-85393200	Weak transcription	Fetal Brain Male	brain

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