Variant report

Variant	rs55684754
Chromosome Location	chr6:34259633-34259634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34251031..34253241-chr6:34259138..34261085,2	MCF-7	breast:
2	chr6:34253205..34255881-chr6:34257864..34260109,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10484267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060308	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10648	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127084	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883137	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883475	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883896	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888452	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628798	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17628946	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994923	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs206922	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269032	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41269034	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269036	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269038	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55694290	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55763242	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798596	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833185	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864834	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56039915	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56107559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309550	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323997	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes]
rs6911272	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7741127	0.80[AMR][1000 genomes]
rs7760373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770443	0.84[EUR][1000 genomes]
rs875274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9368811	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55684754	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34240400-34259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:34240400-34259800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
5	chr6:34241400-34260000	Weak transcription	Esophagus	oesophagus
6	chr6:34244200-34260000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:34245000-34259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:34245000-34260000	Weak transcription	NH-A	brain
10	chr6:34245000-34262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:34245000-34263400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:34245200-34260800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:34245400-34260800	Weak transcription	Aorta	Aorta
14	chr6:34245600-34261600	Weak transcription	Gastric	stomach
15	chr6:34245800-34260000	Weak transcription	HSMMtube	muscle
16	chr6:34246000-34264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:34246600-34264000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:34246600-34264000	Strong transcription	Dnd41	blood
19	chr6:34247400-34259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:34247800-34260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:34249400-34259800	Weak transcription	Fetal Lung	lung
22	chr6:34250600-34261000	Weak transcription	Colonic Mucosa	Colon
23	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr6:34252200-34259800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:34252200-34259800	Weak transcription	Fetal Brain Male	brain
26	chr6:34253000-34259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:34253000-34259800	Weak transcription	Pancreas	Pancrea
28	chr6:34253000-34259800	Weak transcription	HMEC	breast
29	chr6:34253000-34260800	Weak transcription	A549	lung
30	chr6:34253400-34259800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:34253600-34259800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:34253600-34271200	Weak transcription	Stomach Mucosa	stomach
33	chr6:34253800-34259800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:34255000-34263800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr6:34255200-34263800	Strong transcription	Fetal Stomach	stomach
36	chr6:34255600-34260000	Weak transcription	HSMM	muscle
37	chr6:34255600-34260800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:34255800-34259800	Weak transcription	Liver	Liver
39	chr6:34256000-34259800	Weak transcription	NHLF	lung
40	chr6:34256400-34259800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:34256600-34260600	Weak transcription	Thymus	Thymus
42	chr6:34256600-34260800	Weak transcription	Fetal Brain Female	brain
43	chr6:34256600-34264400	Weak transcription	Right Atrium	heart
44	chr6:34256800-34259800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:34256800-34259800	Weak transcription	Hela-S3	cervix
46	chr6:34256800-34260600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:34256800-34260800	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:34256800-34261000	Weak transcription	Small Intestine	intestine
49	chr6:34257000-34259800	Weak transcription	Brain Germinal Matrix	brain
50	chr6:34257000-34260000	Weak transcription	Brain Anterior Caudate	brain

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