Variant report

Variant	rs10408168
Chromosome Location	chr19:20232854-20232855
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:20232731-20232857	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000224864	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10402115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402155	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402722	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404469	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404767	1.00[AMR][1000 genomes]
rs10405110	1.00[AMR][1000 genomes]
rs10406434	1.00[AMR][1000 genomes]
rs10406552	1.00[AMR][1000 genomes]
rs10406926	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408369	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408777	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410951	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412006	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412042	1.00[AMR][1000 genomes]
rs10413166	1.00[AMR][1000 genomes]
rs10414005	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414093	1.00[AMR][1000 genomes]
rs10414627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419576	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420381	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420815	1.00[AMR][1000 genomes]
rs10421160	1.00[AMR][1000 genomes]
rs10421320	1.00[AMR][1000 genomes]
rs10422287	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422539	0.82[AFR][1000 genomes]
rs10424049	1.00[AMR][1000 genomes]
rs10424101	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10427104	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13343888	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13344384	1.00[AMR][1000 genomes]
rs13344637	0.85[AFR][1000 genomes]
rs13345082	1.00[AMR][1000 genomes]
rs2017452	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402094	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28447348	1.00[AMR][1000 genomes]
rs28507750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28514435	1.00[AMR][1000 genomes]
rs28567705	1.00[AMR][1000 genomes]
rs28690849	1.00[AMR][1000 genomes]
rs28767893	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28828686	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59440664	1.00[AMR][1000 genomes]
rs9967629	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking 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 miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
10	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
13	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
15	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
17	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
18	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
19	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
20	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20207600-20240400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:20207600-20240600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:20207600-20241200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:20209400-20239000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:20211400-20238800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:20215200-20240400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:20217000-20238400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
8	chr19:20217200-20234400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr19:20217800-20237200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:20219600-20234200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
11	chr19:20219600-20234800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:20222600-20238800	ZNF genes & repeats	Fetal Lung	lung
13	chr19:20223200-20234400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr19:20226600-20233000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:20226600-20234800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:20226600-20236600	ZNF genes & repeats	Liver	Liver
17	chr19:20226600-20238800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:20228600-20234400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:20229000-20233000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:20230200-20234000	Weak transcription	Fetal Kidney	kidney
21	chr19:20231400-20234000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:20231800-20234400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:20232000-20233000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:20232000-20233000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:20232000-20233000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
26	chr19:20232000-20233000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
27	chr19:20232000-20233000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:20232000-20233000	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr19:20232000-20233000	ZNF genes & repeats	Fetal Stomach	stomach
30	chr19:20232000-20233000	ZNF genes & repeats	Ovary	ovary
31	chr19:20232000-20233000	ZNF genes & repeats	Pancreas	Pancrea
32	chr19:20232000-20233600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:20232000-20237600	ZNF genes & repeats	Fetal Brain Female	brain
34	chr19:20232000-20238400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:20232200-20233800	Weak transcription	Fetal Brain Male	brain
36	chr19:20232200-20234200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr19:20232200-20234200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr19:20232200-20235800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:20232400-20233000	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr19:20232400-20233800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr19:20232800-20233000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:20232800-20233000	ZNF genes & repeats	Left Ventricle	heart
43	chr19:20232800-20234400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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