Variant report

Variant	rs34016523
Chromosome Location	chr4:119557333-119557334
allele	A/T
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	chr4:119557249-119557897	HepG2	liver:	n/a	n/a
2	FOSL2	chr4:119557170-119557609	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:119557310-119557476	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:119557273-119557667	K562	blood:	n/a	n/a
5	POLR2A	chr4:119557325-119557547	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:119557110-119557491	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:119557303-119558743	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251155	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12651650	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34766719	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35183273	1.00[ASN][1000 genomes]
rs35731099	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4001330	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67276048	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67655207	0.99[ASN][1000 genomes]
rs6833597	1.00[ASN][1000 genomes]
rs6855978	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71241793	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs71610209	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71610221	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9760578	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1002771	chr4:119125361-119571237	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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 target site	28 gene(s)	inside rSNPs	diseases
3	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv980251	chr4:119510579-119563981	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1824927	chr4:119521936-119577466	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv966369	chr4:119539088-119559938	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1822873	chr4:119542500-119577466	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv16226	chr4:119552399-119584340	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs34016523	RP11-384K6.6	cis	Adipose Subcutaneous	GTEx
rs34016523	RP11-384K6.2	cis	Adipose Subcutaneous	GTEx
rs34016523	RP11-384K6.6	cis	lung	GTEx
rs34016523	RP11-384K6.2	cis	Artery Tibial	GTEx
rs34016523	RP11-384K6.6	cis	Artery Tibial	GTEx
rs34016523	RP11-384K6.2	cis	Thyroid	GTEx
rs34016523	RP11-384K6.6	cis	Esophagus Mucosa	GTEx
rs34016523	RP11-384K6.2	cis	Nerve Tibial	GTEx
rs34016523	RP11-384K6.2	cis	Whole Blood	GTEx
rs34016523	RP11-384K6.6	cis	Thyroid	GTEx
rs34016523	RP11-384K6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs34016523	RP11-384K6.6	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119513600-119559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:119519800-119559000	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:119528800-119558000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:119549200-119557800	Strong transcription	Fetal Stomach	stomach
5	chr4:119549600-119557600	Strong transcription	Fetal Intestine Small	intestine
6	chr4:119550400-119559000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:119551200-119557800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:119551600-119557800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:119553200-119558000	Weak transcription	Left Ventricle	heart
10	chr4:119553400-119557400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:119553400-119558000	Weak transcription	Fetal Thymus	thymus
12	chr4:119553400-119559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:119553600-119558000	Weak transcription	Thymus	Thymus
14	chr4:119554400-119559000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:119554800-119559000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:119554800-119560400	Weak transcription	Fetal Brain Female	brain
17	chr4:119555600-119558000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:119555600-119558200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:119555600-119559000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:119555600-119559200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:119555600-119559200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:119555800-119557400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr4:119555800-119557400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:119555800-119557400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:119555800-119557400	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:119555800-119557400	Weak transcription	Lung	lung
27	chr4:119555800-119557800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:119555800-119557800	Weak transcription	Fetal Intestine Large	intestine
29	chr4:119555800-119558000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:119555800-119558000	Weak transcription	Liver	Liver
31	chr4:119555800-119558200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:119555800-119558200	Weak transcription	Brain Germinal Matrix	brain
33	chr4:119555800-119559000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:119555800-119559000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:119555800-119559000	Weak transcription	Spleen	Spleen
36	chr4:119555800-119559200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:119556000-119558200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:119556000-119558200	Weak transcription	Gastric	stomach
39	chr4:119556000-119559400	Weak transcription	Placenta	Placenta
40	chr4:119556400-119558000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:119556600-119558400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:119556800-119558400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:119556800-119558400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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