Variant report

Variant	rs41413246
Chromosome Location	chr3:85029725-85029726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:85029590..85031359-chr3:85035312..85037118,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1248853	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1248855	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1248856	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1248863	0.94[EUR][1000 genomes]
rs17022239	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17479424	1.00[EUR][1000 genomes]
rs424029	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7647140	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1000793	chr3:85020452-85051839	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85020000-85030400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:85020000-85030600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:85020200-85032200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:85027600-85030800	Enhancers	Brain Substantia Nigra	brain
5	chr3:85027800-85030000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:85028400-85033800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:85028600-85030800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:85029000-85029800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:85029000-85029800	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr3:85029200-85029800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:85029200-85029800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:85029200-85030000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:85029200-85030000	Enhancers	Fetal Lung	lung
14	chr3:85029400-85030000	Enhancers	Fetal Heart	heart
15	chr3:85029400-85030000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:85029400-85031000	Enhancers	Brain Angular Gyrus	brain
17	chr3:85029400-85036600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:85029600-85029800	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr3:85029600-85030800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:85029600-85030800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:85029600-85031000	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:85029600-85032600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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