Variant report

Variant	rs10406335
Chromosome Location	chr19:44633953-44633954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF226-1	chr19:44632607-44634853	NONHSAT066667

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10408901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410306	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs10413195	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10413511	0.91[ASN][1000 genomes]
rs10420143	0.88[EUR][1000 genomes]
rs10853771	0.99[ASN][1000 genomes]
rs1236712	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1236715	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1236716	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2061332	0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2061333	0.91[CHB][hapmap];0.90[CHD][hapmap]
rs2068061	0.83[TSI][hapmap]
rs2168778	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284981	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2356750	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446946	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28539456	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3172	0.81[CHB][hapmap]
rs3746319	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs4239529	0.83[CHB][hapmap]
rs4429390	0.83[CHB][hapmap]
rs4459653	0.83[CHB][hapmap]
rs4508518	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4802206	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs4802207	0.81[CHB][hapmap]
rs4802208	0.99[ASN][1000 genomes]
rs4803676	0.83[CHB][hapmap];0.83[TSI][hapmap]
rs7250004	0.88[EUR][1000 genomes]
rs7250005	0.86[EUR][1000 genomes]
rs7251868	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253485	0.99[ASN][1000 genomes]
rs7508149	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs7508762	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099869	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs8104573	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs8105860	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs8113750	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9304638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10406335	GRIN2D	cis	cerebellum	SCAN
rs10406335	ETFB	cis	parietal	SCAN
rs10406335	SNORD34	cis	parietal	SCAN
rs10406335	CLPTM1	cis	cerebellum	SCAN
rs10406335	TULP2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44618200-44635000	Weak transcription	Stomach Mucosa	stomach
2	chr19:44618600-44635000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:44618800-44635000	Weak transcription	HMEC	breast
4	chr19:44619600-44637200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:44619600-44638600	ZNF genes & repeats	Liver	Liver
6	chr19:44619800-44635000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:44620000-44634600	Strong transcription	Brain Hippocampus Middle	brain
8	chr19:44620000-44635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:44620400-44635000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:44620400-44635000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:44622800-44636800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:44622800-44645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:44623400-44637200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr19:44623400-44637800	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr19:44623400-44638800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:44623800-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:44623800-44640600	Weak transcription	HepG2	liver
18	chr19:44624000-44635000	Weak transcription	Fetal Heart	heart
19	chr19:44624200-44637400	ZNF genes & repeats	Fetal Lung	lung
20	chr19:44624800-44635800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr19:44625400-44639000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr19:44626000-44637000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
23	chr19:44626200-44636000	Strong transcription	Brain Angular Gyrus	brain
24	chr19:44626400-44634600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
25	chr19:44626800-44636600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr19:44627000-44634600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr19:44627600-44636000	Strong transcription	Brain Anterior Caudate	brain
28	chr19:44628000-44635200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:44628600-44636400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr19:44628800-44635800	Strong transcription	Brain Cingulate Gyrus	brain
31	chr19:44628800-44636000	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:44628800-44636800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr19:44628800-44636800	Strong transcription	Dnd41	blood
34	chr19:44629000-44634000	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:44629200-44635000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr19:44629800-44634400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr19:44629800-44635000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:44630000-44634200	Strong transcription	Fetal Kidney	kidney
39	chr19:44630000-44636000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:44630000-44636400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:44630000-44636800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:44630200-44634200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:44630200-44634200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:44630200-44635000	Strong transcription	Osteobl	bone
45	chr19:44630200-44635200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:44630200-44636400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
47	chr19:44630200-44636800	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr19:44630200-44636800	ZNF genes & repeats	Ovary	ovary
49	chr19:44630200-44637000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:44630400-44634400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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