Variant report

Variant	rs56338425
Chromosome Location	chr2:133896307-133896308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10496698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11896774	0.87[AFR][1000 genomes]
rs11899352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11901784	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs16857050	0.84[AMR][1000 genomes]
rs16857164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16857175	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16857181	0.81[AMR][1000 genomes]
rs16857210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16857345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16857928	1.00[AMR][1000 genomes]
rs2117307	0.81[AFR][1000 genomes]
rs4954030	0.81[AFR][1000 genomes]
rs55665571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56737980	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59288803	0.81[AMR][1000 genomes]
rs59500613	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61188333	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72998828	0.81[AMR][1000 genomes]
rs72998840	0.81[AMR][1000 genomes]
rs72998879	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72998896	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73000811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000815	0.91[AMR][1000 genomes]
rs73000831	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73000868	0.84[AMR][1000 genomes]
rs73956704	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916805	chr2:133664765-133924973	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv834381	chr2:133722671-133897994	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv875139	chr2:133777866-133929225	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv949546	chr2:133798832-133933491	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv875140	chr2:133816484-133904829	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1008004	chr2:133827250-133954810	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv949629	chr2:133830379-134014961	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1001601	chr2:133838626-134005959	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv948851	chr2:133864452-133955999	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv583167	chr2:133864452-133957689	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv834383	chr2:133874257-133906766	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
14	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133884400-133896600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:133885800-133897800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:133887800-133896400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:133887800-133912600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:133889000-133896400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:133892200-133897200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:133892200-133897800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:133893000-133897000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:133894200-133897800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:133895200-133896400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:133895400-133898000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:133895600-133897000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:133895800-133897400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:133895800-133898600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:133896000-133897200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:133896000-133899400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:133896200-133896400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
18	chr2:133896200-133896800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr2:133896200-133897000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr2:133896200-133897200	Enhancers	Brain Substantia Nigra	brain
21	chr2:133896200-133899800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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