Variant report

Variant	rs10200879
Chromosome Location	chr2:111963246-111963247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10174361	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10197366	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10197465	0.81[EUR][1000 genomes]
rs10207669	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10209377	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12329287	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12619474	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12711874	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12989775	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13400065	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13411196	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13431908	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13432448	0.94[CEU][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1398029	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1398030	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464024	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35520250	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35565356	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4616483	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4848426	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10200879	CHCHD5	cis	cerebellum	SCAN
rs10200879	CKAP2L	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111950200-111969600	Weak transcription	Dnd41	blood
2	chr2:111952200-111974800	Weak transcription	Aorta	Aorta
3	chr2:111952600-111963600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:111952600-111965200	Weak transcription	Fetal Intestine Small	intestine
5	chr2:111953000-111968000	Weak transcription	K562	blood
6	chr2:111954800-112006800	Weak transcription	HUVEC	blood vessel
7	chr2:111955200-111963400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:111957200-111972400	Weak transcription	NHLF	lung
9	chr2:111958000-111974400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:111958400-111967600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:111958400-111968600	Weak transcription	HepG2	liver
12	chr2:111958400-111972000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:111958400-111974200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:111959200-111964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:111959200-111966000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:111960600-111966000	Weak transcription	HSMMtube	muscle
17	chr2:111960600-111966400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:111960800-111965400	Weak transcription	Osteobl	bone
19	chr2:111960800-111965600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:111960800-111965600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:111961200-111964600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:111961400-111965400	Weak transcription	NHDF-Ad	bronchial
23	chr2:111962000-111966200	Weak transcription	NH-A	brain
24	chr2:111962200-111965000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:111962600-111964400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:111962600-111965800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:111962600-111974400	Weak transcription	Left Ventricle	heart
28	chr2:111962800-111965000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:111963000-111963800	Strong transcription	HSMM	muscle

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