Variant report

Variant	rs10875752
Chromosome Location	chr12:48554636-48554637
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	chr12:48554610-48554949	GM12891	blood:	n/a	chr12:48554785-48554798 chr12:48554787-48554796 chr12:48554788-48554795
2	SPI1	chr12:48554522-48555076	HL-60	blood:	n/a	chr12:48554785-48554798 chr12:48554787-48554796 chr12:48554788-48554795
3	GATA1	chr12:48554213-48555189	PBDE	blood:	n/a	chr12:48554364-48554372
4	SPI1	chr12:48554564-48554921	GM12891	blood:	n/a	chr12:48554785-48554798 chr12:48554787-48554796 chr12:48554788-48554795

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1049392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747529	1.00[JPT][hapmap]
rs10875733	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs10875739	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10875754	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875759	0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875765	0.87[ASN][1000 genomes]
rs10875766	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168350	0.94[JPT][hapmap]
rs11168353	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168363	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168364	0.81[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168373	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11168378	0.82[EUR][1000 genomes]
rs11168404	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs11168412	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs11168419	0.84[ASN][1000 genomes]
rs11168424	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168438	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168439	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11168442	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168443	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11168444	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168445	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168446	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168447	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168448	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168453	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11168454	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11834818	0.83[EUR][1000 genomes]
rs12228924	0.90[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12422355	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12425679	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12426981	0.85[EUR][1000 genomes]
rs17122567	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1859443	0.94[JPT][hapmap]
rs1978161	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2171643	0.87[ASN][1000 genomes]
rs2286020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291483	0.90[MEX][hapmap]
rs2408954	1.00[JPT][hapmap]
rs3742075	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs3825403	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4258439	1.00[JPT][hapmap]
rs56097189	0.91[ASN][1000 genomes]
rs57430775	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58540891	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58556309	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59537300	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580658	0.88[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs66507954	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7132898	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7133274	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7136243	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7136782	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7136788	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7299704	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7302354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7303677	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs73104071	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73105950	0.88[ASN][1000 genomes]
rs73304926	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7484942	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs765260	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7962390	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962569	0.81[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8181670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs886589	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs954326	0.94[JPT][hapmap]
rs9651981	0.96[GIH][hapmap];0.94[JPT][hapmap]
rs9804751	0.96[GIH][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10875752	TMEM106C	cis	parietal	SCAN
rs10875752	C12orf41	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48552000-48555800	Enhancers	Primary hematopoietic stem cells	blood
2	chr12:48552000-48556600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:48552000-48557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:48552200-48554800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:48552200-48554800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr12:48552200-48556600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr12:48552800-48556000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr12:48553800-48555000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:48553800-48555400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:48553800-48555600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr12:48553800-48555600	Enhancers	GM12878-XiMat	blood
12	chr12:48554000-48554800	Enhancers	Brain Hippocampus Middle	brain
13	chr12:48554000-48555200	Enhancers	Brain Cingulate Gyrus	brain
14	chr12:48554000-48555600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:48554000-48555600	Enhancers	Fetal Heart	heart
16	chr12:48554000-48555800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:48554200-48555400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:48554400-48554800	Enhancers	Brain Germinal Matrix	brain
19	chr12:48554400-48555000	Enhancers	Brain Anterior Caudate	brain
20	chr12:48554600-48554800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:48554600-48554800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:48554600-48554800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:48554600-48554800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:48554600-48554800	Enhancers	Adipose Nuclei	Adipose
25	chr12:48554600-48554800	Enhancers	Esophagus	oesophagus
26	chr12:48554600-48554800	Enhancers	Fetal Thymus	thymus
27	chr12:48554600-48554800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr12:48554600-48555000	Enhancers	Fetal Lung	lung
29	chr12:48554600-48555000	Enhancers	Fetal Muscle Trunk	muscle
30	chr12:48554600-48555200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:48554600-48555400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:48554600-48556000	Enhancers	K562	blood
33	chr12:48554600-48556600	Enhancers	Psoas Muscle	Psoas
34	chr12:48554600-48557000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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