Variant report

Variant	rs59832183
Chromosome Location	chr6:34245035-34245036
allele	C/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	chr6:34244390-34246326	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:34244615-34245055	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:34244327-34250971	K562	blood:	n/a	n/a
4	POLR2A	chr6:34244995-34245040	HepG2	liver:	n/a	n/a
5	MAX	chr6:34244635-34245058	HepG2	liver:	n/a	n/a
6	CUX1	chr6:34244487-34245599	K562	blood:	n/a	n/a
7	GATA2	chr6:34244980-34245553	K562	blood:	n/a	chr6:34245329-34245339 chr6:34245328-34245344 chr6:34245332-34245341 chr6:34245332-34245339 chr6:34245325-34245346 chr6:34245332-34245339 chr6:34245331-34245341 chr6:34245332-34245339
8	MAX	chr6:34244487-34245090	K562	blood:	n/a	n/a
9	POLR2A	chr6:34244646-34246351	PFSK-1	brain:	n/a	n/a
10	ZNF263	chr6:34244598-34245575	HEK293-T-REx	kidney:	n/a	chr6:34244818-34244839 chr6:34244832-34244841
11	TBL1XR1	chr6:34244774-34245515	K562	blood:	n/a	n/a
12	BHLHE40	chr6:34244803-34245502	K562	blood:	n/a	n/a
13	RXRA	chr6:34244457-34245125	HepG2	liver:	n/a	chr6:34244596-34244610
14	MYC	chr6:34244625-34245643	K562	blood:	n/a	chr6:34245404-34245413 chr6:34245409-34245417 chr6:34245406-34245416 chr6:34245406-34245415 chr6:34245406-34245415 chr6:34245406-34245415
15	EP300	chr6:34244979-34245569	K562	blood:	n/a	n/a
16	TEAD4	chr6:34244906-34245718	K562	blood:	n/a	n/a
17	TEAD4	chr6:34244884-34245692	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:34232764..34235632-chr6:34243482..34245527,2	MCF-7	breast:
2	chr6:34243756..34245812-chr6:34390841..34393824,2	K562	blood:
3	chr6:34243359..34245671-chr6:34250933..34253670,2	MCF-7	breast:
4	chr6:34239800..34242616-chr6:34243635..34245743,3	K562	blood:
5	chr6:34211942..34216855-chr6:34244859..34247946,7	K562	blood:

Variant related genes	Relation type
ENSG00000225339	TF binding region
ENSG00000124614	Chromatin interaction
ENSG00000186577	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10440840	0.87[EUR][1000 genomes]
rs10484267	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10484268	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1057691	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1060308	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10648	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1127084	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1265	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12654	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13466	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16883137	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16883475	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16883896	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16888452	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17628798	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17628946	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17629180	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17629270	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17696583	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17696774	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17696829	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1994923	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs206922	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3798554	0.84[AMR][1000 genomes]
rs3798557	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41269032	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41269034	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41269036	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41269038	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55674397	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55684754	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55694290	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55763242	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55779010	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55798596	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55812200	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55833185	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55863933	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55864834	0.90[AMR][1000 genomes]
rs56033036	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56039915	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56107559	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56188036	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56274913	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56309550	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56323997	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56330729	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6911272	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73420934	0.91[AFR][1000 genomes]
rs73420942	0.95[EUR][1000 genomes]
rs7738665	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7760373	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs875274	0.88[AMR][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	nsv885781	chr6:34110257-34247661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv885784	chr6:34187206-34246714	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv3377596	chr6:34243274-34247372	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59832183	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34218200-34255000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:34228600-34247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:34229000-34246800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:34231200-34246600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:34233000-34251800	Weak transcription	NHDF-Ad	bronchial
6	chr6:34233200-34245400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:34234200-34247600	Weak transcription	Brain Germinal Matrix	brain
8	chr6:34235800-34245600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:34237000-34246600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:34238400-34259400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:34239000-34247600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:34239200-34246000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:34239600-34247000	Weak transcription	Fetal Brain Female	brain
14	chr6:34239800-34245400	Weak transcription	Fetal Stomach	stomach
15	chr6:34240000-34246200	Enhancers	Left Ventricle	heart
16	chr6:34240200-34245400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:34240200-34249000	Weak transcription	NHLF	lung
18	chr6:34240200-34250200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:34240200-34255200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:34240400-34249600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:34240400-34251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:34240400-34255000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:34240400-34259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:34240400-34259800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:34240600-34246000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:34240600-34247200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:34240600-34250400	Weak transcription	Brain Substantia Nigra	brain
28	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
30	chr6:34241000-34248600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr6:34241200-34245600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:34241400-34245800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:34241400-34246600	Weak transcription	Fetal Intestine Small	intestine
34	chr6:34241400-34260000	Weak transcription	Esophagus	oesophagus
35	chr6:34241600-34245400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:34241600-34245400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:34241600-34246600	Weak transcription	Dnd41	blood
38	chr6:34241600-34249600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:34241600-34250400	Weak transcription	Fetal Thymus	thymus
40	chr6:34241600-34252800	Weak transcription	Stomach Mucosa	stomach
41	chr6:34241800-34245600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:34241800-34245600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:34241800-34246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:34241800-34247800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:34242000-34246600	Weak transcription	Spleen	Spleen
46	chr6:34242000-34247000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:34242000-34252800	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:34242200-34245600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:34242200-34246400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:34242200-34246400	Weak transcription	Monocytes-CD14+_RO01746	blood

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