Variant report

Variant	rs12196021
Chromosome Location	chr6:69375013-69375014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:69369127..69370671-chr6:69372780..69375655,2	K562	blood:
2	chr6:69374562..69377202-chr6:69385965..69388256,2	K562	blood:
3	chr6:68749500..68752266-chr6:69373788..69375882,2	K562	blood:
4	chr6:69373114..69378102-chr6:69378626..69382768,5	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10945134	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes]
rs12194992	1.00[CEU][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2024561	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2254150	0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2256337	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs2585593	0.81[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2585594	0.96[CEU][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2585618	1.00[JPT][hapmap]
rs2746126	0.82[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2746129	0.85[EUR][1000 genomes]
rs2802699	1.00[JPT][hapmap]
rs2802705	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs28395490	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4554295	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs4607402	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs478070	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs530888	0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs639338	0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs6908159	0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs6930275	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7753280	0.84[EUR][1000 genomes]
rs9342729	0.90[JPT][hapmap]
rs9342730	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9342731	0.96[CEU][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9346233	1.00[CEU][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9346234	0.84[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs9346236	0.96[EUR][1000 genomes]
rs9346237	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9346238	0.92[JPT][hapmap]
rs9351734	0.96[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9351735	0.81[EUR][1000 genomes]
rs9351736	0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs9363962	0.91[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12196021	RP3-525N10.2	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69352200-69399000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:69364200-69399800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:69365800-69377400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr6:69367600-69377600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:69368400-69377800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:69368600-69376000	Weak transcription	K562	blood
7	chr6:69372400-69376200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:69374800-69382800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:69375000-69382800	Weak transcription	Fetal Lung	lung

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