Variant report

Variant	rs3729837
Chromosome Location	chr19:55668397-55668398
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	SIN3A	chr19:55667439-55668479	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:55667406-55669499	K562	blood:	n/a	n/a
3	SP4	chr19:55667620-55668443	H1-hESC	embryonic stem cell:	n/a	chr19:55667918-55667934 chr19:55667916-55667932 chr19:55667918-55667929 chr19:55667899-55667915 chr19:55668151-55668167 chr19:55667901-55667912 chr19:55668319-55668335 chr19:55667847-55667863 chr19:55667869-55667885 chr19:55667867-55667883 chr19:55668321-55668337
4	POLR2A	chr19:55668112-55668475	HCT-116	colon:	n/a	n/a
5	SP1	chr19:55667587-55668401	A549	lung:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55668344-55668356 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55668344-55668356 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336
6	CCNT2	chr19:55668316-55668520	K562	blood:	n/a	chr19:55668323-55668332
7	POLR2A	chr19:55668174-55668504	HCT-116	colon:	n/a	n/a
8	ELF1	chr19:55668253-55668518	K562	blood:	n/a	n/a
9	SP1	chr19:55667311-55668566	H1-hESC	embryonic stem cell:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55668344-55668356 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55668344-55668356 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336
10	ZBTB7A	chr19:55668048-55669871	K562	blood:	n/a	n/a
11	IRF1	chr19:55667643-55668435	K562	blood:	n/a	chr19:55668319-55668333 chr19:55668151-55668165 chr19:55667916-55667930 chr19:55667867-55667881
12	ELF1	chr19:55667636-55668411	K562	blood:	n/a	n/a
13	NFYB	chr19:55667979-55668481	K562	blood:	n/a	n/a
14	MAZ	chr19:55667600-55668496	K562	blood:	n/a	chr19:55668118-55668127
15	CHD2	chr19:55668003-55668437	H1-hESC	embryonic stem cell:	n/a	chr19:55668346-55668356
16	HDAC2	chr19:55668290-55668508	K562	blood:	n/a	n/a
17	POLR2A	chr19:55667494-55668614	SK-N-MC	brain:	n/a	n/a
18	ZBTB7A	chr19:55667485-55670788	K562	blood:	n/a	n/a
19	REST	chr19:55668012-55668473	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55667256..55669360-chr19:55970897..55972567,2	K562	blood:
2	chr19:55598098..55602192-chr19:55668353..55672028,4	K562	blood:
3	chr19:55666494..55670422-chr19:55672733..55675574,3	K562	blood:
4	chr19:55658387..55665037-chr19:55666866..55670836,8	K562	blood:
5	chr19:55666595..55669878-chr19:55917801..55921094,4	K562	blood:
6	chr19:55627602..55630542-chr19:55666165..55668443,2	K562	blood:
7	chr19:55655324..55657835-chr19:55666870..55669444,2	K562	blood:
8	chr19:55666873..55668722-chr19:55676430..55678695,2	K562	blood:
9	chr19:55627370..55629030-chr19:55666382..55669249,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNNI3-1	chr19:55668097-55668496	NONHSAT067996

Variant related genes	Relation type
ENSG00000267577	TF binding region
TNNI3	TF binding region
ENSG00000125503	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000105048	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10424609	0.91[ASN][1000 genomes]
rs10424638	1.00[ASN][1000 genomes]
rs11669300	0.88[ASN][1000 genomes]
rs11670538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672000	0.88[ASN][1000 genomes]
rs11672834	0.88[ASN][1000 genomes]
rs13343638	0.85[ASN][1000 genomes]
rs16986289	1.00[ASN][1000 genomes]
rs16986292	1.00[ASN][1000 genomes]
rs16986294	1.00[ASN][1000 genomes]
rs3729841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859540	1.00[ASN][1000 genomes]
rs3859542	1.00[ASN][1000 genomes]
rs6509927	1.00[ASN][1000 genomes]
rs6509930	0.96[ASN][1000 genomes]
rs7248799	1.00[ASN][1000 genomes]
rs8107129	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8107736	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110415	0.91[ASN][1000 genomes]
rs9749340	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55666400-55669400	Active TSS	Left Ventricle	heart
2	chr19:55667200-55668400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr19:55667200-55668400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:55667200-55668400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:55667200-55668600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
6	chr19:55667200-55668600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:55667200-55668800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr19:55667200-55669200	Active TSS	Right Atrium	heart
9	chr19:55667400-55668400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr19:55667400-55668400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
11	chr19:55667400-55668400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:55667400-55668400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
13	chr19:55667400-55668400	Active TSS	A549	lung
14	chr19:55667400-55668600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:55667400-55668600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr19:55667400-55668600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:55667400-55668600	Enhancers	Gastric	stomach
18	chr19:55667400-55668600	Enhancers	Pancreas	Pancrea
19	chr19:55667400-55668800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:55667400-55668800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:55667400-55668800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:55667400-55668800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr19:55667400-55668800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:55667400-55668800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr19:55667400-55668800	Bivalent/Poised TSS	HepG2	liver
26	chr19:55667400-55669000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr19:55667400-55669000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr19:55667400-55669000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
29	chr19:55667400-55669000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr19:55667400-55669000	ZNF genes & repeats	Spleen	Spleen
31	chr19:55667400-55669200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr19:55667400-55669400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr19:55667400-55670000	Bivalent Enhancer	Placenta	Placenta
34	chr19:55667600-55668400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:55667600-55668400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:55667600-55668400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:55667600-55668400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:55667600-55668600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:55667600-55668600	Bivalent Enhancer	Esophagus	oesophagus
40	chr19:55667600-55668600	Bivalent Enhancer	Fetal Brain Male	brain
41	chr19:55667600-55669000	Active TSS	Fetal Heart	heart
42	chr19:55667800-55668400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:55667800-55668400	Bivalent Enhancer	Brain Anterior Caudate	brain
44	chr19:55667800-55668400	Bivalent Enhancer	Fetal Stomach	stomach
45	chr19:55667800-55668400	Bivalent Enhancer	Stomach Mucosa	stomach
46	chr19:55667800-55668400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
47	chr19:55667800-55668600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:55667800-55668600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
49	chr19:55667800-55668600	Bivalent Enhancer	Fetal Intestine Large	intestine
50	chr19:55667800-55668800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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