Variant report

Variant	rs28622316
Chromosome Location	chr19:19908211-19908212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10401290	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10401847	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10401908	1.00[EUR][1000 genomes]
rs10402267	1.00[EUR][1000 genomes]
rs10405029	1.00[EUR][1000 genomes]
rs10407581	1.00[EUR][1000 genomes]
rs10408499	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408890	1.00[EUR][1000 genomes]
rs10409568	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411668	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412298	1.00[EUR][1000 genomes]
rs10414667	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416020	1.00[EUR][1000 genomes]
rs10419073	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423312	1.00[EUR][1000 genomes]
rs10423574	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423992	1.00[EUR][1000 genomes]
rs10425214	1.00[EUR][1000 genomes]
rs11878325	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879946	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880495	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880971	1.00[EUR][1000 genomes]
rs11880972	1.00[EUR][1000 genomes]
rs11880975	1.00[EUR][1000 genomes]
rs11881233	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11881507	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346878	1.00[EUR][1000 genomes]
rs16996376	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437283	1.00[EUR][1000 genomes]
rs28655627	1.00[EUR][1000 genomes]
rs28668259	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28696819	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28698719	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45447205	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55870166	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56413930	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57018770	1.00[EUR][1000 genomes]
rs57405289	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57691007	1.00[EUR][1000 genomes]
rs59586774	1.00[EUR][1000 genomes]
rs60287284	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250673	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251735	1.00[EUR][1000 genomes]
rs73526738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73526768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73526771	0.86[AMR][1000 genomes]
rs73528913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73528956	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73923028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73925538	1.00[EUR][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:104 , 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	chr19:19888600-19909000	Weak transcription	K562	blood
3	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
4	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
5	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:19895600-19909000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr19:19895600-19909000	ZNF genes & repeats	Liver	Liver
10	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr19:19895800-19914800	Strong transcription	Dnd41	blood
13	chr19:19896000-19909200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:19897200-19908600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr19:19897200-19918600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:19900000-19915200	Weak transcription	HepG2	liver
17	chr19:19901000-19909000	ZNF genes & repeats	GM12878-XiMat	blood
18	chr19:19902000-19914400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
20	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:19902800-19910200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:19903000-19908400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
23	chr19:19903200-19916400	Weak transcription	Fetal Brain Male	brain
24	chr19:19903800-19911000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:19903800-19911000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
26	chr19:19904000-19908400	ZNF genes & repeats	Fetal Intestine Large	intestine
27	chr19:19904200-19908400	ZNF genes & repeats	Primary B cells from cord blood	blood
28	chr19:19904200-19908800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:19904200-19908800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:19904200-19909200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr19:19904400-19908600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr19:19904600-19908400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
33	chr19:19904600-19909000	ZNF genes & repeats	Fetal Lung	lung
34	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:19905200-19909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:19905600-19909000	Strong transcription	Osteobl	bone
37	chr19:19905600-19913600	Weak transcription	Brain Substantia Nigra	brain
38	chr19:19905800-19910400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:19906000-19908600	Weak transcription	HSMM	muscle
40	chr19:19906000-19908800	Strong transcription	Brain Germinal Matrix	brain
41	chr19:19906200-19914000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:19906400-19908400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr19:19906400-19920400	Weak transcription	Brain Angular Gyrus	brain
44	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:19906600-19908400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr19:19906600-19908400	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:19906800-19908400	ZNF genes & repeats	Fetal Stomach	stomach
48	chr19:19906800-19910400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:19906800-19916200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:19907000-19908800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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