Variant report

Variant	rs12754784
Chromosome Location	chr1:210869187-210869188
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210849903..210852743-chr1:210867034..210869915,2	K562	blood:
2	chr1:210846826..210848354-chr1:210867968..210870812,2	K562	blood:
3	chr1:210865698..210867541-chr1:210869096..210870691,2	K562	blood:
4	chr1:210865100..210867541-chr1:210867654..210870691,4	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12735867	0.82[AMR][1000 genomes]
rs12754319	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs17188444	0.82[AMR][1000 genomes]
rs17188465	0.82[AMR][1000 genomes]
rs17260648	0.82[AMR][1000 genomes]
rs34689382	0.82[AMR][1000 genomes]
rs34700735	0.82[AMR][1000 genomes]
rs35007206	0.82[AMR][1000 genomes]
rs35486198	0.82[AMR][1000 genomes]
rs35504217	0.82[AMR][1000 genomes]
rs35751839	0.82[AMR][1000 genomes]
rs35936572	0.82[AMR][1000 genomes]
rs61827458	0.82[AMR][1000 genomes]
rs61827459	0.82[AMR][1000 genomes]
rs61829465	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873150	chr1:210808270-210893233	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv468083	chr1:210854815-210876192	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv549123	chr1:210854815-210876192	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12754784	NSL1	cis	parietal	SCAN
rs12754784	CIB1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210838000-210880400	Weak transcription	Gastric	stomach
2	chr1:210846400-210884600	Weak transcription	Ovary	ovary
3	chr1:210857200-210882600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:210857800-210870800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:210858000-210880400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:210864400-210889800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:210865200-210869800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:210865600-210869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:210865600-210870600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:210865800-210869400	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:210866000-210869800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:210866200-210870800	Enhancers	HSMMtube	muscle
13	chr1:210866600-210869400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:210866800-210869400	Weak transcription	GM12878-XiMat	blood
15	chr1:210866800-210872000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:210866800-210884800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:210868000-210871200	Enhancers	HSMM	muscle
18	chr1:210868200-210869200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:210868800-210869200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:210869000-210869200	Enhancers	Brain Anterior Caudate	brain
21	chr1:210869000-210869800	Enhancers	Fetal Lung	lung
22	chr1:210869000-210871200	Enhancers	Fetal Muscle Leg	muscle

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