Variant report

Variant	rs2018392
Chromosome Location	chr19:18990982-18990983
allele	A/G
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	chr19:18990827-18991314	SK-N-MC	brain:	n/a	n/a
2	IRF1	chr19:18990310-18991210	K562	blood:	n/a	chr19:18990805-18990819 chr19:18990912-18990926 chr19:18990982-18990996 chr19:18991004-18991018
3	STAT3	chr19:18990798-18990997	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:18988598-18991468	MCF-7	breast:	n/a	n/a
5	SP4	chr19:18990177-18991203	H1-hESC	embryonic stem cell:	n/a	chr19:18991006-18991022 chr19:18990805-18990821 chr19:18990984-18991000 chr19:18991004-18991020 chr19:18990982-18990998 chr19:18990912-18990928 chr19:18990807-18990818
6	STAT3	chr19:18990417-18990999	MCF10A-Er-Src	breast:	n/a	n/a
7	EGR1	chr19:18990080-18991112	K562	blood:	n/a	chr19:18990987-18991000 chr19:18990985-18990995
8	MAX	chr19:18990935-18991359	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr19:18990733-18990984	K562	blood:	n/a	n/a
10	MAZ	chr19:18990517-18991137	K562	blood:	n/a	n/a
11	MAX	chr19:18990741-18991204	K562	blood:	n/a	n/a
12	SIN3A	chr19:18990941-18991143	H1-hESC	embryonic stem cell:	n/a	n/a
13	ELF1	chr19:18990494-18991122	K562	blood:	n/a	chr19:18990979-18990991
14	POLR2A	chr19:18988692-18991381	Hela-S3	cervix:	n/a	n/a
15	SP1	chr19:18990404-18991230	H1-hESC	embryonic stem cell:	n/a	chr19:18990915-18990929 chr19:18990807-18990819 chr19:18990984-18990996 chr19:18990947-18990959 chr19:18990914-18990926 chr19:18990986-18990995 chr19:18990916-18990925 chr19:18990915-18990924 chr19:18990914-18990926 chr19:18990984-18990996 chr19:18991007-18991016 chr19:18990808-18990817 chr19:18990947-18990959 chr19:18990915-18990925 chr19:18990809-18990818 chr19:18991006-18991018 chr19:18990948-18990957 chr19:18990807-18990818 chr19:18990915-18990925 chr19:18990915-18990924 chr19:18990808-18990822 chr19:18990985-18990999 chr19:18991006-18991018 chr19:18990949-18990958 chr19:18990985-18990994 chr19:18990807-18990819 chr19:18991012-18991019
16	CHD2	chr19:18990897-18991061	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:18990604-18991323	ECC-1	luminal epithelium:	n/a	n/a
18	SP4	chr19:18990472-18991179	H1-hESC	embryonic stem cell:	n/a	chr19:18991006-18991022 chr19:18990805-18990821 chr19:18990984-18991000 chr19:18991004-18991020 chr19:18990982-18990998 chr19:18990912-18990928 chr19:18990807-18990818
19	POLR2A	chr19:18990853-18991314	ECC-1	luminal epithelium:	n/a	n/a
20	EGR1	chr19:18990658-18991092	K562	blood:	n/a	chr19:18990987-18991000 chr19:18990985-18990995
21	POLR2A	chr19:18990689-18991102	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18989707..18992076-chr19:19050980..19053421,2	K562	blood:
2	chr19:18990686..18992268-chr19:19005562..19008438,2	K562	blood:
3	chr19:18965705..18968424-chr19:18988642..18991060,2	K562	blood:
4	chr19:18990686..18992579-chr19:19006938..19009413,2	K562	blood:
5	chr19:18990848..18992488-chr19:19028769..19030378,2	K562	blood:
6	chr19:18981741..18983441-chr19:18990489..18991991,2	K562	blood:
7	chr19:18984024..18987729-chr19:18988322..18991283,4	K562	blood:
8	chr19:18989338..18991884-chr19:19005552..19007379,3	MCF-7	breast:
9	chr19:18941192..18944158-chr19:18989151..18991227,3	K562	blood:
10	chr19:18973585..18975733-chr19:18989912..18992220,3	K562	blood:
11	chr19:18990660..18992183-chr19:19041463..19043164,2	K562	blood:
12	chr19:18960692..18962403-chr19:18990602..18992305,2	K562	blood:

Variant related genes	Relation type
ENSG00000269694	TF binding region
ENSG00000105669	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000269019	Chromatin interaction
ENSG00000223802	Chromatin interaction
ENSG00000130283	Chromatin interaction
ENSG00000005007	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10410987	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11673194	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2005695	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808161	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808163	0.87[EUR][1000 genomes]
rs4808164	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4808866	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808868	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808869	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4808870	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57870078	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7250661	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7252523	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252796	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257086	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73526907	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73526909	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757114	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs886298	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv828473	chr19:18975130-18994875	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18979600-18991800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr19:18980400-19004000	Weak transcription	Psoas Muscle	Psoas
3	chr19:18980400-19004200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:18981400-18998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:18981800-18997800	Weak transcription	Ovary	ovary
6	chr19:18981800-19005800	Weak transcription	Right Atrium	heart
7	chr19:18982000-18991400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:18982000-19002200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:18982400-18995200	Strong transcription	Brain Anterior Caudate	brain
10	chr19:18982600-19000800	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:18983400-18998200	Strong transcription	Brain Cingulate Gyrus	brain
12	chr19:18984000-18995600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:18984000-19004200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:18984600-18995000	Strong transcription	Brain Hippocampus Middle	brain
15	chr19:18984800-18995200	Strong transcription	Brain Angular Gyrus	brain
16	chr19:18984800-18995200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:18985600-19004400	Weak transcription	Fetal Brain Male	brain
18	chr19:18986600-18995000	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:18987200-19004200	Weak transcription	HSMMtube	muscle
20	chr19:18987400-18991000	Weak transcription	Fetal Kidney	kidney
21	chr19:18988000-18991000	Weak transcription	Hela-S3	cervix
22	chr19:18988000-18995200	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr19:18988000-19005400	Weak transcription	A549	lung
24	chr19:18988200-18993000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:18988200-18993800	Weak transcription	Aorta	Aorta
26	chr19:18988200-18994400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:18988200-18995600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:18988200-19004800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:18988400-18991000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:18988400-18992000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:18988400-18995200	Strong transcription	Brain Germinal Matrix	brain
32	chr19:18988400-18995200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr19:18988400-18995200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr19:18988400-18996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:18988400-18998400	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:18988600-18991000	Weak transcription	Placenta	Placenta
37	chr19:18988800-18994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:18989000-18991200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:18989000-18991200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr19:18989200-18999000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:18989200-18999200	Strong transcription	Fetal Brain Female	brain
42	chr19:18989400-18991200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:18989600-18991000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr19:18989600-18991000	Weak transcription	Colonic Mucosa	Colon
45	chr19:18989800-18991200	Weak transcription	Fetal Intestine Small	intestine
46	chr19:18989800-18991400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:18989800-18991400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:18989800-18994000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr19:18989800-18994200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:18989800-18994600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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