Variant report

Variant	rs12260489
Chromosome Location	chr10:25394305-25394306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10508681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11014322	1.00[EUR][1000 genomes]
rs11014406	1.00[EUR][1000 genomes]
rs12245315	1.00[EUR][1000 genomes]
rs12246243	1.00[EUR][1000 genomes]
rs12247487	1.00[EUR][1000 genomes]
rs12247642	1.00[EUR][1000 genomes]
rs12249087	1.00[EUR][1000 genomes]
rs12250135	1.00[EUR][1000 genomes]
rs12251969	1.00[EUR][1000 genomes]
rs12260419	1.00[EUR][1000 genomes]
rs12261956	1.00[EUR][1000 genomes]
rs12265350	1.00[EUR][1000 genomes]
rs16925216	1.00[EUR][1000 genomes]
rs16925349	1.00[EUR][1000 genomes]
rs16925371	0.81[AMR][1000 genomes]
rs16925389	1.00[EUR][1000 genomes]
rs16925393	1.00[EUR][1000 genomes]
rs1873737	1.00[EUR][1000 genomes]
rs1926053	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1926054	0.81[AMR][1000 genomes]
rs28475481	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4330994	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57480457	1.00[EUR][1000 genomes]
rs57542069	1.00[EUR][1000 genomes]
rs7086600	1.00[EUR][1000 genomes]
rs7097598	1.00[EUR][1000 genomes]
rs74123298	1.00[EUR][1000 genomes]
rs74123299	1.00[EUR][1000 genomes]
rs74123300	1.00[EUR][1000 genomes]
rs7894458	1.00[EUR][1000 genomes]
rs7916898	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036683	chr10:25337592-25398119	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv894969	chr10:25345720-25395579	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv894970	chr10:25385858-25522280	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25388800-25394400	Enhancers	Fetal Brain Male	brain
2	chr10:25388800-25395200	Enhancers	Fetal Brain Female	brain
3	chr10:25389800-25394600	Enhancers	Brain Germinal Matrix	brain
4	chr10:25390600-25394600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:25390600-25395000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr10:25392200-25397000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr10:25392400-25414200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:25393200-25395000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:25393400-25395200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:25393400-25395400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr10:25393400-25395600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr10:25393400-25398400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr10:25393600-25394600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr10:25393600-25394600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr10:25393600-25395000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr10:25393600-25395800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr10:25393800-25395000	Enhancers	Brain Anterior Caudate	brain
18	chr10:25393800-25395400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr10:25394000-25394800	Weak transcription	Brain Substantia Nigra	brain
20	chr10:25394000-25402000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr10:25394200-25395000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:25394200-25395000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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