Variant report

Variant	rs1322142
Chromosome Location	chr9:10233361-10233362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10217572	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10217711	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10217805	0.85[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs10738156	0.85[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10756010	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10809036	0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10809037	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10809039	1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10809042	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10809043	0.85[EUR][1000 genomes]
rs10809044	0.84[CEU][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10809045	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes]
rs10958964	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10958965	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10958968	0.93[EUR][1000 genomes]
rs12353282	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1322143	0.89[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13300585	0.82[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1407348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1407349	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1407913	0.82[CHB][hapmap]
rs1590264	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1885431	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2890914	0.85[EUR][1000 genomes]
rs4143460	0.86[CHB][hapmap]
rs4741019	0.81[CHB][hapmap]
rs56381014	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61314978	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7846730	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs7866028	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034731	chr9:9776126-10481262	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv892295	chr9:9832245-10380406	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1030657	chr9:10002355-10481262	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1033178	chr9:10169848-10428731	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv471280	chr9:10172572-10277602	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv466158	chr9:10172573-10277602	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613375	chr9:10172573-10277602	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2758179	chr9:10188450-10370398	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2759666	chr9:10188450-10370398	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv892310	chr9:10197122-10279606	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1034040	chr9:10225500-10255910	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv892311	chr9:10226620-10265282	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv892312	chr9:10231178-10279606	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:10231400-10234200	Enhancers	Fetal Brain Male	brain
2	chr9:10231800-10234000	Enhancers	Fetal Brain Female	brain
3	chr9:10232000-10233400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:10232000-10233400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr9:10232400-10233400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:10232400-10233600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr9:10232400-10233600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:10232400-10234000	Enhancers	Brain Germinal Matrix	brain
9	chr9:10232600-10233400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:10232600-10233400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:10232800-10233400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:10233000-10233400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr9:10233000-10233400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr9:10233200-10238000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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