Variant report

Variant	rs10413195
Chromosome Location	chr19:44634903-44634904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10406335	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]
rs10408901	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10410306	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10413511	0.90[ASN][1000 genomes]
rs10420143	0.87[EUR][1000 genomes]
rs10853771	0.98[ASN][1000 genomes]
rs1236712	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1236715	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs1236716	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs2061332	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs2061333	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs2168778	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284980	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284981	0.91[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs2356750	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28446946	0.86[EUR][1000 genomes]
rs28539456	0.86[EUR][1000 genomes]
rs3746319	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs4508518	0.81[CHD][hapmap]
rs4802206	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4802208	0.97[ASN][1000 genomes]
rs7250004	0.87[EUR][1000 genomes]
rs7250005	0.85[EUR][1000 genomes]
rs7251868	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253485	0.98[ASN][1000 genomes]
rs7508149	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7508762	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8099869	0.91[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs8104573	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8105860	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8113750	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9304638	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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
rs10413195	GRIN2D	cis	cerebellum	SCAN
rs10413195	CLPTM1	cis	cerebellum	SCAN
rs10413195	SNORD34	cis	parietal	SCAN
rs10413195	TULP2	cis	cerebellum	SCAN
rs10413195	ETFB	cis	parietal	SCAN

Chromatin state (count:121 , 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	chr19:44620000-44635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:44620400-44635000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:44620400-44635000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:44622800-44636800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:44622800-44645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:44623400-44637200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr19:44623400-44637800	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr19:44623400-44638800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:44623800-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:44623800-44640600	Weak transcription	HepG2	liver
17	chr19:44624000-44635000	Weak transcription	Fetal Heart	heart
18	chr19:44624200-44637400	ZNF genes & repeats	Fetal Lung	lung
19	chr19:44624800-44635800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr19:44625400-44639000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr19:44626000-44637000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:44626200-44636000	Strong transcription	Brain Angular Gyrus	brain
23	chr19:44626800-44636600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr19:44627600-44636000	Strong transcription	Brain Anterior Caudate	brain
25	chr19:44628000-44635200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:44628600-44636400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr19:44628800-44635800	Strong transcription	Brain Cingulate Gyrus	brain
28	chr19:44628800-44636000	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr19:44628800-44636800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
30	chr19:44628800-44636800	Strong transcription	Dnd41	blood
31	chr19:44629200-44635000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:44629800-44635000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:44630000-44636000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:44630000-44636400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:44630000-44636800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:44630200-44635000	Strong transcription	Osteobl	bone
37	chr19:44630200-44635200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:44630200-44636400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
39	chr19:44630200-44636800	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr19:44630200-44636800	ZNF genes & repeats	Ovary	ovary
41	chr19:44630200-44637000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:44630400-44635800	Strong transcription	Placenta	Placenta
43	chr19:44630400-44636400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr19:44630400-44636800	ZNF genes & repeats	Aorta	Aorta
45	chr19:44630400-44637200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:44630400-44637200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:44630600-44637600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
48	chr19:44630600-44645000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:44631000-44636600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:44631000-44637200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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