Variant report

Variant	rs10418932
Chromosome Location	chr19:40800288-40800289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40791303..40794605-chr19:40798342..40800635,3	K562	blood:

Variant related genes	Relation type
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10408356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415181	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10416620	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419465	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420842	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10422343	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10423896	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12151243	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs16974157	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163840	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304188	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28362958	0.93[ASN][1000 genomes]
rs28667591	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34716810	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55862427	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57885763	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58336440	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58613082	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59010363	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59343080	0.84[ASN][1000 genomes]
rs60869669	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61685259	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62107590	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62107593	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107594	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107630	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107631	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247916	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248861	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7254617	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73044533	0.88[ASN][1000 genomes]
rs8100207	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111619	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112998	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs892118	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892119	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs892120	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304588	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304589	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934426	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv3386713	chr19:40794161-40828617	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10418932	DEDD2	cis	cerebellum	SCAN
rs10418932	RPL18	cis	parietal	SCAN
rs10418932	PSG8	cis	parietal	SCAN
rs10418932	EML2	cis	cerebellum	SCAN
rs10418932	APOC4	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40792000-40802600	Weak transcription	Fetal Brain Female	brain
2	chr19:40792000-40807600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:40792000-40811400	Weak transcription	Brain Anterior Caudate	brain
4	chr19:40792000-40826200	Weak transcription	Hela-S3	cervix
5	chr19:40792200-40807600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:40792200-40810200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:40792200-40821400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:40792200-40821400	Weak transcription	Fetal Intestine Small	intestine
9	chr19:40792400-40802200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:40793000-40805400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr19:40793000-40810200	Weak transcription	Adipose Nuclei	Adipose
12	chr19:40793000-40821400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:40793000-40822000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr19:40793200-40820600	Weak transcription	HSMM	muscle
15	chr19:40793200-40820800	Weak transcription	Dnd41	blood
16	chr19:40793200-40822000	Weak transcription	Fetal Stomach	stomach
17	chr19:40793800-40821800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:40798800-40800400	Weak transcription	HepG2	liver
19	chr19:40799000-40801200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:40799800-40800800	Weak transcription	Thymus	Thymus
21	chr19:40800000-40800400	Enhancers	Brain Angular Gyrus	brain
22	chr19:40800000-40800800	Enhancers	Brain Hippocampus Middle	brain
23	chr19:40800000-40800800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:40800000-40801000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr19:40800000-40801000	Enhancers	Brain Substantia Nigra	brain
26	chr19:40800200-40801000	Enhancers	Brain Cingulate Gyrus	brain

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