Variant report

Variant	rs946961
Chromosome Location	chr10:23094828-23094829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:23090832..23093813-chr10:23094691..23097138,2	K562	blood:
2	chr10:23092682..23094839-chr2:187127661..187130019,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10764345	0.86[EUR][1000 genomes]
rs10828335	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10828336	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10828337	0.86[EUR][1000 genomes]
rs11013140	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1538887	0.88[EUR][1000 genomes]
rs1572850	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222871	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4534468	0.94[ASN][1000 genomes]
rs4748823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6482239	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6482240	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7078904	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7080378	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7083521	0.82[JPT][hapmap]
rs7085974	0.95[ASN][1000 genomes]
rs7093389	0.87[EUR][1000 genomes]
rs7098985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7894952	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7898655	0.87[EUR][1000 genomes]
rs7908924	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875598	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
rs946961	ABI1	cis	parietal	SCAN
rs946961	C10orf67	cis	parietal	SCAN
rs946961	BMI1	cis	parietal	SCAN
rs946961	APBB1IP	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23090800-23095000	Enhancers	NHDF-Ad	bronchial
2	chr10:23091600-23095800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:23091600-23096000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:23091800-23095000	Enhancers	HSMMtube	muscle
5	chr10:23092000-23095800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:23092200-23095400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:23092400-23095000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr10:23092800-23095400	Enhancers	Brain Substantia Nigra	brain
9	chr10:23093000-23099600	Weak transcription	NH-A	brain
10	chr10:23093000-23105200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:23093600-23095000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:23093600-23095200	Enhancers	Fetal Intestine Small	intestine
13	chr10:23093600-23095600	Enhancers	Fetal Stomach	stomach
14	chr10:23093800-23095000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:23093800-23095000	Enhancers	Brain Germinal Matrix	brain
16	chr10:23093800-23095000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr10:23093800-23095000	Enhancers	Fetal Brain Female	brain
18	chr10:23093800-23095000	Enhancers	Fetal Heart	heart
19	chr10:23093800-23096400	Enhancers	Colon Smooth Muscle	Colon
20	chr10:23094000-23095000	Enhancers	Fetal Kidney	kidney
21	chr10:23094000-23095000	Enhancers	HSMM	muscle
22	chr10:23094200-23095000	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr10:23094200-23095400	Enhancers	Fetal Brain Male	brain
24	chr10:23094400-23095000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr10:23094400-23095000	Enhancers	Placenta	Placenta
26	chr10:23094400-23095000	Enhancers	Right Atrium	heart
27	chr10:23094400-23095400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr10:23094400-23095800	Enhancers	Rectal Smooth Muscle	rectum
29	chr10:23094600-23095000	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr10:23094600-23095000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr10:23094600-23099600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:23094600-23099600	Weak transcription	NHLF	lung
33	chr10:23094800-23095000	Enhancers	Brain Angular Gyrus	brain
34	chr10:23094800-23095600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:23094800-23095600	Enhancers	Brain Cingulate Gyrus	brain
36	chr10:23094800-23104400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:23094800-23105200	Weak transcription	Osteobl	bone

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