Variant report

Variant	rs12554298
Chromosome Location	chr9:9754602-9754603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10816172	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10816175	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10816176	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816177	0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10977937	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10977939	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10977941	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10977945	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10977946	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10977947	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10977948	0.89[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10977952	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10977953	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10977954	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10977956	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10977957	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10977963	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10977964	0.90[ASN][1000 genomes]
rs10977970	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1174579	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1174583	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1174584	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1174585	0.95[ASN][1000 genomes]
rs1174586	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12236463	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12236514	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12238315	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12238410	1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12551715	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12552265	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12553611	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12554427	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12554588	0.83[JPT][hapmap]
rs12554796	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12555110	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12555408	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12684484	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12686088	0.82[JPT][hapmap]
rs12686662	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1408119	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1408120	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1408121	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1408122	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs16924740	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2147068	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2209193	0.91[EUR][1000 genomes]
rs2211134	0.82[JPT][hapmap]
rs2252236	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2252243	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2382039	0.82[JPT][hapmap]
rs2761710	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2761762	1.00[YRI][hapmap]
rs2821505	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2821512	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2821513	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4490896	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs4740986	0.81[JPT][hapmap]
rs4742615	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742616	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742618	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs724330	0.90[ASN][1000 genomes]
rs981790	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033808	chr9:9431799-9777960	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv892264	chr9:9440838-9796577	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892265	chr9:9476425-9796116	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv892270	chr9:9591059-9860735	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv613319	chr9:9630855-9778653	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1028772	chr9:9631694-9779358	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2422381	chr9:9647540-9887820	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1020468	chr9:9658670-9780975	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv539983	chr9:9658670-9780975	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv892274	chr9:9687742-9787587	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv526471	chr9:9718066-9832245	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv613321	chr9:9724976-9758609	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1034236	chr9:9728895-9779358	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2829906	chr9:9737201-9897866	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9752200-9754800	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr9:9754200-9755200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr9:9754400-9755000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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