Variant report

Variant	rs12065394
Chromosome Location	chr1:175039603-175039604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:175028783..175030971-chr1:175038361..175041126,2	K562	blood:
2	chr1:175037331..175039889-chr1:175047402..175050144,2	K562	blood:
3	chr1:175037717..175040130-chr1:175044107..175046974,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10798330	0.89[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap]
rs10912888	0.89[CHB][hapmap];0.91[GIH][hapmap]
rs11577778	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578942	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11578961	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11582121	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11583313	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11583729	0.89[CHB][hapmap];0.91[GIH][hapmap]
rs12059398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068402	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068982	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12076122	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12083779	0.89[CHB][hapmap]
rs16847779	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17302688	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17374668	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4466606	0.89[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs4625241	0.89[CHB][hapmap];0.91[GIH][hapmap]
rs55808408	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55967803	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56226643	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59822966	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61541139	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6665471	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695255	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703193	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515773	0.89[CHB][hapmap];0.91[GIH][hapmap]
rs7546260	0.89[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap]
rs9650986	0.93[AMR][1000 genomes];0.98[EUR][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	nsv1011472	chr1:175013165-175042885	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1012861	chr1:175021780-175063160	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv535210	chr1:175021780-175063160	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv825487	chr1:175031609-175113572	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12065394	KLHL20	cis	parietal	SCAN
rs12065394	DNM3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175036800-175041000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:175037200-175040200	Weak transcription	Fetal Stomach	stomach
3	chr1:175037200-175040600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:175037200-175041000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:175037200-175041000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:175037200-175041000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:175037200-175041400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:175037400-175039800	Weak transcription	Adipose Nuclei	Adipose
9	chr1:175038000-175041200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:175038200-175041000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:175038600-175041000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:175039200-175040200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:175039200-175041400	Enhancers	Fetal Muscle Leg	muscle
14	chr1:175039600-175040000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:175039600-175041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:175039600-175041200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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