Variant report

Variant	rs7975693
Chromosome Location	chr12:40588678-40588679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:40588670-40589049	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
LRRK2	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10454013	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs10877929	0.85[JPT][hapmap]
rs11174735	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11174998	0.80[ASN][1000 genomes]
rs11175021	0.80[ASN][1000 genomes]
rs11175027	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs11175090	0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs11175094	0.83[JPT][hapmap]
rs11175106	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs11175409	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11175456	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11175843	1.00[YRI][hapmap]
rs11175935	1.00[YRI][hapmap]
rs11564157	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11564215	0.81[EUR][1000 genomes]
rs12228213	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12230685	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs17491786	1.00[YRI][hapmap]
rs17519594	1.00[YRI][hapmap]
rs2201142	0.86[ASN][1000 genomes]
rs2708445	0.82[ASN][1000 genomes]
rs28370645	0.85[JPT][hapmap]
rs28370647	0.85[JPT][hapmap]
rs28370666	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs4533099	0.86[ASN][1000 genomes]
rs61933163	0.86[ASN][1000 genomes]
rs7135815	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs7301226	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302006	0.92[MKK][hapmap]
rs7953143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7966132	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966741	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7969677	0.89[GIH][hapmap]
rs7973688	0.92[EUR][1000 genomes];0.91[ASN][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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40586000-40591000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr12:40586200-40591600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:40586800-40588800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:40587200-40589400	Weak transcription	HUVEC	blood vessel
5	chr12:40587200-40590400	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:40588000-40590400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:40588200-40589400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr12:40588200-40589400	Weak transcription	Primary B cells from cord blood	blood
9	chr12:40588200-40589400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:40588400-40589600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr12:40588600-40590400	Enhancers	Primary hematopoietic stem cells	blood

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