Variant report

Variant	rs10422280
Chromosome Location	chr19:40313214-40313215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40312822..40314907-chr19:40475908..40478539,3	MCF-7	breast:
2	chr19:40306242..40311061-chr19:40311644..40314932,5	K562	blood:
3	chr19:40311807..40313522-chr19:40320426..40322337,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYRK1B-1	chr19:40312166-40313894	NONHSAT066323

Variant related genes	Relation type
ENSG00000105204	Chromatin interaction
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11880094	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880956	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11883249	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459589	0.81[GIH][hapmap]
rs12975624	0.85[CHB][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs12980289	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986299	0.83[CHB][hapmap]
rs2072290	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354471	0.81[GIH][hapmap]
rs2354800	0.96[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810383	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810386	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs616650	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62106867	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508912	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508913	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718066	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246501	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247063	0.81[GIH][hapmap]
rs7248926	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250408	0.82[GIH][hapmap]
rs7253739	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254914	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10422280	B9D2	cis	cerebellum	SCAN
rs10422280	PHLDB3	cis	parietal	SCAN
rs10422280	ERF	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40296200-40314200	Weak transcription	Right Ventricle	heart
2	chr19:40298800-40314200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:40299800-40313600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:40300200-40314200	Weak transcription	Gastric	stomach
5	chr19:40300800-40313400	Weak transcription	Pancreas	Pancrea
6	chr19:40301600-40314200	Weak transcription	Ovary	ovary
7	chr19:40301600-40314400	Weak transcription	Primary B cells from cord blood	blood
8	chr19:40301600-40314400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:40302600-40314400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:40302800-40314200	Weak transcription	Brain Angular Gyrus	brain
11	chr19:40303000-40314200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr19:40303000-40314200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:40303200-40314200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:40303800-40314200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr19:40304000-40313400	Weak transcription	Brain Germinal Matrix	brain
16	chr19:40304000-40314200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:40304600-40314200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:40304600-40314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:40304600-40314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:40305000-40314200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:40305200-40314200	Weak transcription	Thymus	Thymus
22	chr19:40305200-40314200	Weak transcription	NHLF	lung
23	chr19:40305400-40314200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:40305400-40314200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:40305800-40314200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:40305800-40314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:40306000-40314200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:40306000-40314200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:40306000-40314200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:40306000-40314400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:40306200-40313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:40306200-40314200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:40306200-40314200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:40306200-40314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:40306400-40314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:40306600-40314200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:40306600-40314200	Weak transcription	HSMM	muscle
38	chr19:40306800-40313800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:40306800-40314200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:40306800-40314400	Weak transcription	NHEK	skin
41	chr19:40307000-40313600	Weak transcription	Fetal Brain Male	brain
42	chr19:40307200-40314200	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:40307200-40314200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr19:40307400-40313600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:40307400-40314400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:40307600-40313600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:40307600-40314200	Weak transcription	Lung	lung
48	chr19:40307600-40314400	Weak transcription	Aorta	Aorta
49	chr19:40308000-40314000	Weak transcription	Adipose Nuclei	Adipose
50	chr19:40308200-40314000	Weak transcription	NH-A	brain

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