Variant report

Variant	rs1080090
Chromosome Location	chr19:20210022-20210023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10405913	0.81[ASN][1000 genomes]
rs10409169	0.91[ASN][1000 genomes]
rs10415451	0.91[ASN][1000 genomes]
rs10419563	0.91[ASN][1000 genomes]
rs10421131	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10422858	0.80[EUR][1000 genomes]
rs10424553	0.80[ASN][1000 genomes]
rs10425448	0.91[ASN][1000 genomes]
rs11085297	0.81[ASN][1000 genomes]
rs11882897	0.81[ASN][1000 genomes]
rs12459967	0.90[ASN][1000 genomes]
rs12461434	0.91[ASN][1000 genomes]
rs2217650	0.86[ASN][1000 genomes]
rs57885738	0.81[ASN][1000 genomes]
rs59724513	0.81[ASN][1000 genomes]
rs6511078	0.81[ASN][1000 genomes]
rs7246986	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7249909	0.91[ASN][1000 genomes]
rs7249965	0.91[ASN][1000 genomes]
rs7250100	0.90[ASN][1000 genomes]
rs7254910	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7507883	0.91[ASN][1000 genomes]
rs8101678	0.91[ASN][1000 genomes]
rs8109748	0.81[ASN][1000 genomes]
rs8112652	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20190400-20211400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:20192000-20210200	Weak transcription	Ovary	ovary
3	chr19:20198600-20211200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:20198600-20211400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:20205000-20211200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:20207600-20210400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:20207600-20211400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:20207600-20213800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
9	chr19:20207600-20214400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:20207600-20216800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
11	chr19:20207600-20240400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:20207600-20240600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:20207600-20241200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:20207800-20210400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:20207800-20210800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:20207800-20211400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr19:20207800-20216800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr19:20207800-20218400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:20208000-20222400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:20208200-20211200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:20209200-20210200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:20209200-20214400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr19:20209400-20210200	ZNF genes & repeats	Fetal Stomach	stomach
24	chr19:20209400-20213600	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr19:20209400-20221800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:20209400-20239000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:20209600-20211200	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr19:20209600-20211800	Weak transcription	Left Ventricle	heart
29	chr19:20209800-20213200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:20209800-20213600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr19:20210000-20210200	Genic enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:20210000-20210400	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr19:20210000-20210800	Strong transcription	Fetal Lung	lung
34	chr19:20210000-20213600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
35	chr19:20210000-20214000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
36	chr19:20210000-20218000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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