Variant report

Variant	rs7854273
Chromosome Location	chr9:3427166-3427167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:105111195..105111695-chr9:3426799..3427334,2	NB4	blood:
2	chr9:3426927..3428604-chr9:3430165..3432458,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10115757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10115791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs10117846	0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10124295	0.86[CHB][hapmap]
rs10814082	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10814096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10814097	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10971665	0.89[CHB][hapmap]
rs10971685	0.89[JPT][hapmap]
rs10971976	0.88[EUR][1000 genomes]
rs10972042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10972081	0.81[AMR][1000 genomes]
rs12115798	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12337095	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12339955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12340535	0.88[ASW][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap]
rs12341652	0.89[JPT][hapmap]
rs12341737	0.89[JPT][hapmap];0.83[TSI][hapmap]
rs12346432	0.89[JPT][hapmap]
rs12347985	0.88[CHD][hapmap];0.89[TSI][hapmap]
rs12554323	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs13287892	0.91[ASN][1000 genomes]
rs13290412	0.89[JPT][hapmap]
rs13295925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13297034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13298219	0.89[JPT][hapmap]
rs13298908	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13300358	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs13302841	0.88[JPT][hapmap]
rs16924266	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1998976	0.81[CHD][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap]
rs34065256	0.81[ASN][1000 genomes]
rs34331766	0.81[ASN][1000 genomes]
rs3758195	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3758196	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs4741829	0.90[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs60796901	0.81[ASN][1000 genomes]
rs6476436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7022711	0.81[JPT][hapmap]
rs7024933	0.90[JPT][hapmap]
rs7028812	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs7040113	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.96[ASN][1000 genomes]
rs7041836	0.89[JPT][hapmap]
rs7850576	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7853728	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7864440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7864459	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs9695619	0.88[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	esv3349329	chr9:3426502-3428550	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3403639	chr9:3426952-3428100	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
2	chr9:3398800-3437200	Weak transcription	Primary B cells from cord blood	blood
3	chr9:3412000-3434600	Weak transcription	Ovary	ovary
4	chr9:3419000-3437000	Weak transcription	Brain Substantia Nigra	brain
5	chr9:3420200-3427800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:3422600-3436800	Weak transcription	Psoas Muscle	Psoas
7	chr9:3425000-3428000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:3425600-3453200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:3426600-3444600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:3426800-3429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:3426800-3432400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:3426800-3434600	Weak transcription	Primary T cells from cord blood	blood
13	chr9:3426800-3437000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:3426800-3446200	Weak transcription	Left Ventricle	heart
15	chr9:3427000-3436600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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