Variant report

Variant	rs4741829
Chromosome Location	chr9:3412419-3412420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10115757	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10115791	0.85[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs10117357	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10117431	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10117846	0.85[CEU][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10124292	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10124295	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10814019	0.87[EUR][1000 genomes]
rs10814038	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10814039	0.92[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10814082	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10814096	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10971661	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10971665	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10971685	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10971806	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10972042	0.91[JPT][hapmap]
rs10972079	0.83[CEU][hapmap]
rs10972081	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11536748	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12002215	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs12335763	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12337095	0.85[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12338587	0.89[EUR][1000 genomes]
rs12338927	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12339955	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12340535	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12341652	1.00[CEU][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes]
rs12341737	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12343385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12346432	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs12347811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12347985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12554323	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs13286511	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13290412	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs13295925	0.85[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13297034	0.85[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13298219	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs13298908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13300358	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs13300995	0.82[EUR][1000 genomes]
rs13302664	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13302841	0.83[CEU][hapmap]
rs1348369	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs16924266	0.91[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1998976	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs34065256	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34086781	0.83[EUR][1000 genomes]
rs34233417	0.91[EUR][1000 genomes]
rs34331766	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34708788	0.83[EUR][1000 genomes]
rs34774267	0.81[ASN][1000 genomes]
rs35545940	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35945655	0.85[EUR][1000 genomes]
rs3758195	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758196	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4237147	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4741825	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4741826	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57004251	0.85[EUR][1000 genomes]
rs60796901	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6476436	0.85[CEU][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6476451	0.85[EUR][1000 genomes]
rs66463406	0.89[EUR][1000 genomes]
rs66763574	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7022711	0.92[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7024933	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7028812	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7040113	0.92[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7041836	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs7043493	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs71506639	0.85[EUR][1000 genomes]
rs71506645	0.83[EUR][1000 genomes]
rs7850576	0.81[ASN][1000 genomes]
rs7851558	0.81[JPT][hapmap]
rs7853728	0.90[JPT][hapmap]
rs7854273	0.90[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs7864440	0.91[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7875889	0.92[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9695619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
2	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
3	chr9:3398800-3415400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:3398800-3418600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:3398800-3423400	Weak transcription	Primary T cells from cord blood	blood
6	chr9:3398800-3437200	Weak transcription	Primary B cells from cord blood	blood
7	chr9:3402400-3425000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:3408400-3418000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:3410600-3414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:3410800-3425000	Weak transcription	Brain Germinal Matrix	brain
11	chr9:3411000-3425400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr9:3412000-3434600	Weak transcription	Ovary	ovary
13	chr9:3412400-3415600	Weak transcription	Fetal Heart	heart

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