Variant report

Variant	rs875598
Chromosome Location	chr10:23093282-23093283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:23093031..23094566-chr10:23095292..23097801,2	K562	blood:
2	chr10:23090452..23092008-chr10:23092511..23094369,2	K562	blood:
3	chr10:23092682..23094839-chr2:187127661..187130019,2	MCF-7	breast:
4	chr10:23090832..23093813-chr10:23094691..23097138,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10764345	0.86[EUR][1000 genomes]
rs10828335	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10828336	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10828337	0.86[EUR][1000 genomes]
rs11013140	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1538887	0.89[EUR][1000 genomes]
rs1572850	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222871	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4534468	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4748823	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6482239	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482240	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7078904	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7080378	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7083521	0.82[JPT][hapmap]
rs7084892	0.81[ASN][1000 genomes]
rs7085974	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7093389	0.88[EUR][1000 genomes]
rs7098985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7894952	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7898655	0.86[EUR][1000 genomes]
rs7908924	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946961	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894960	chr10:23049139-23113841	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv894961	chr10:23049139-23128475	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv466833	chr10:23050683-23110797	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv894962	chr10:23050683-23113841	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv894963	chr10:23050683-23121820	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv894964	chr10:23050683-23128475	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv894965	chr10:23071128-23113841	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2764013	chr10:23087298-23239345	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv894966	chr10:23090535-23202522	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs875598	BMI1	cis	parietal	SCAN
rs875598	ABI1	cis	parietal	SCAN
rs875598	C10orf67	cis	parietal	SCAN
rs875598	APBB1IP	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23090800-23094400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:23090800-23095000	Enhancers	NHDF-Ad	bronchial
3	chr10:23091000-23093600	Weak transcription	Fetal Lung	lung
4	chr10:23091000-23093800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr10:23091600-23095800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:23091600-23096000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:23091800-23094800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:23091800-23094800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:23091800-23095000	Enhancers	HSMMtube	muscle
10	chr10:23092000-23093400	Enhancers	Stomach Smooth Muscle	stomach
11	chr10:23092000-23094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr10:23092000-23094600	Enhancers	NHLF	lung
13	chr10:23092000-23095800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:23092200-23095400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:23092400-23093600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr10:23092400-23093800	Weak transcription	Brain Germinal Matrix	brain
17	chr10:23092400-23095000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:23092800-23094600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr10:23092800-23094600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:23092800-23095400	Enhancers	Brain Substantia Nigra	brain
21	chr10:23093000-23093600	Weak transcription	Fetal Stomach	stomach
22	chr10:23093000-23094000	Weak transcription	HSMM	muscle
23	chr10:23093000-23094600	Enhancers	Brain Hippocampus Middle	brain
24	chr10:23093000-23099600	Weak transcription	NH-A	brain
25	chr10:23093000-23105200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr10:23093200-23093600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:23093200-23093600	Weak transcription	Osteobl	bone
28	chr10:23093200-23094400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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