Variant report

Variant	rs10408499
Chromosome Location	chr19:19910596-19910597
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10401290	0.84[AMR][1000 genomes]
rs10401847	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409568	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414667	0.84[AMR][1000 genomes]
rs10419073	0.85[AMR][1000 genomes]
rs10423574	0.84[AMR][1000 genomes]
rs11878325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11879946	0.84[AMR][1000 genomes]
rs11880495	0.84[AMR][1000 genomes]
rs11881233	0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11881507	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11882779	1.00[AMR][1000 genomes]
rs11882889	1.00[AMR][1000 genomes]
rs16996376	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28622316	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28668259	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28696819	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28698719	0.84[AMR][1000 genomes]
rs45447205	0.84[AMR][1000 genomes]
rs55870166	0.84[AMR][1000 genomes]
rs56413930	0.84[AMR][1000 genomes]
rs57405289	0.84[AMR][1000 genomes]
rs60287284	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250673	0.84[AMR][1000 genomes]
rs73526738	0.92[AMR][1000 genomes]
rs73526768	1.00[AMR][1000 genomes]
rs73526771	0.86[AMR][1000 genomes]
rs73528913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73528956	0.84[AMR][1000 genomes]
rs73923028	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv578799	chr19:19901136-19967970	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
2	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
3	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
4	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:19895800-19914800	Strong transcription	Dnd41	blood
10	chr19:19897200-19918600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:19900000-19915200	Weak transcription	HepG2	liver
12	chr19:19902000-19914400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
14	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:19903200-19916400	Weak transcription	Fetal Brain Male	brain
16	chr19:19903800-19911000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:19903800-19911000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:19905600-19913600	Weak transcription	Brain Substantia Nigra	brain
20	chr19:19906200-19914000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:19906400-19920400	Weak transcription	Brain Angular Gyrus	brain
22	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:19906800-19916200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:19907000-19911400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr19:19907000-19911600	Weak transcription	Gastric	stomach
26	chr19:19907000-19913600	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:19907000-19913800	Weak transcription	Placenta	Placenta
28	chr19:19907000-19914000	Weak transcription	Spleen	Spleen
29	chr19:19907000-19914400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:19907000-19916200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:19907000-19916400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:19907000-19923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr19:19907200-19911600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr19:19907200-19912800	Weak transcription	Brain Anterior Caudate	brain
37	chr19:19907200-19913400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr19:19907200-19913600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:19907200-19913600	Weak transcription	Adipose Nuclei	Adipose
40	chr19:19907200-19913600	Weak transcription	HSMMtube	muscle
41	chr19:19907200-19913800	Weak transcription	Ovary	ovary
42	chr19:19907200-19914200	Weak transcription	Pancreas	Pancrea
43	chr19:19907200-19915800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:19907600-19911400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine
46	chr19:19907800-19911200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
49	chr19:19908200-19911200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:19908200-19911200	Weak transcription	Fetal Thymus	thymus

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