Variant report

Variant	rs73040113
Chromosome Location	chr19:36737203-36737204
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	MAX	chr19:36736834-36737283	HUVEC	blood vessel:	n/a	chr19:36737266-36737275
2	USF1	chr19:36736875-36737286	SK-N-SH_RA	brain:	n/a	n/a
3	MAX	chr19:36735969-36737342	H1-hESC	embryonic stem cell:	n/a	chr19:36737266-36737275 chr19:36735971-36735980
4	MYC	chr19:36737186-36737223	MCF-7	breast:	n/a	n/a
5	PBX3	chr19:36736981-36737208	GM12878	blood:	n/a	n/a
6	BCL3	chr19:36736776-36737392	GM12878	blood:	n/a	n/a
7	MXI1	chr19:36735746-36737699	SK-N-SH	brain:	n/a	chr19:36736524-36736533
8	TCF3	chr19:36736786-36737361	GM12878	blood:	n/a	n/a
9	CEBPB	chr19:36737188-36737309	A549	lung:	n/a	n/a
10	CEBPB	chr19:36737103-36737306	IMR90	lung:	n/a	n/a
11	NFATC1	chr19:36736860-36737307	GM12878	blood:	n/a	n/a
12	MXI1	chr19:36736305-36737639	IMR90	lung:	n/a	chr19:36736524-36736533
13	BCL3	chr19:36736809-36737328	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ZNF565	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10407835	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10407850	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10409983	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10412832	0.84[ASN][1000 genomes]
rs10415410	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10416509	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10416742	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419269	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425166	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11882933	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12459704	0.84[ASN][1000 genomes]
rs12460466	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12461077	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12461112	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12461855	0.82[AFR][1000 genomes]
rs12463157	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28414272	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28528757	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806284	0.80[EUR][1000 genomes]
rs4806293	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4806294	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806295	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806303	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55697131	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56316708	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56686317	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58395495	0.89[EUR][1000 genomes]
rs59026641	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59295196	0.82[ASN][1000 genomes]
rs61413061	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62113146	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62113148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62113149	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62113151	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62113152	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7251745	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73038028	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73040107	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73040148	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73041817	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8106135	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8113088	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs73040113	LINC00665	cis	Nerve Tibial	GTEx
rs73040113	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs73040113	LINC00665	cis	Muscle Skeletal	GTEx
rs73040113	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36730400-36748400	Weak transcription	HSMMtube	muscle
2	chr19:36734600-36737800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:36734800-36737400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:36734800-36737600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:36735800-36737400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr19:36735800-36737400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr19:36735800-36737400	Active TSS	Rectal Smooth Muscle	rectum
8	chr19:36735800-36737600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:36735800-36737600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
10	chr19:36735800-36737600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:36735800-36737800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
12	chr19:36736000-36737400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:36736000-36737400	ZNF genes & repeats	Lung	lung
14	chr19:36736000-36737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
15	chr19:36736000-36737400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
16	chr19:36736000-36737400	ZNF genes & repeats	Spleen	Spleen
17	chr19:36736000-36737600	ZNF genes & repeats	Pancreas	Pancrea
18	chr19:36736000-36737800	ZNF genes & repeats	Liver	Liver
19	chr19:36736200-36737400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
20	chr19:36736200-36737400	ZNF genes & repeats	Esophagus	oesophagus
21	chr19:36736200-36737400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
22	chr19:36736200-36737600	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr19:36736200-36746200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:36736400-36737400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:36736600-36738800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:36736600-36739200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr19:36736800-36737400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr19:36736800-36737400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr19:36736800-36737400	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr19:36736800-36737400	Bivalent Enhancer	Fetal Heart	heart
31	chr19:36736800-36737600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:36736800-36738000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr19:36736800-36738000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr19:36737000-36737400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr19:36737000-36737400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:36737000-36737400	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr19:36737000-36737400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:36737000-36737400	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr19:36737000-36737400	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
40	chr19:36737000-36737400	Bivalent/Poised TSS	Fetal Kidney	kidney
41	chr19:36737000-36737400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:36737000-36737600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr19:36737000-36737600	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr19:36737000-36737800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr19:36737200-36737400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:36737200-36737400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:36737200-36737400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:36737200-36737400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:36737200-36737400	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
50	chr19:36737200-36737400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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