Variant report

Variant	rs56330729
Chromosome Location	chr6:34321050-34321051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34318109..34321086-chr6:34360029..34361626,2	MCF-7	breast:
2	chr6:34320498..34323149-chr6:34325939..34328541,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPS10-2	chr6:34320586-34321981	predAs_engstrom06_BI253382_1

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10484267	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484268	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1057691	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1060308	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10648	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1127084	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1265	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13466	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883137	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883475	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883896	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888452	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17628798	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17628946	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629180	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629270	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696583	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696774	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696829	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994923	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs206922	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798554	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269032	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41269034	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269036	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269038	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55684754	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55694290	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55763242	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55779010	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55798596	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55812200	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55833185	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55864834	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56039915	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56107559	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56188036	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56274913	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309550	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56323997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59832183	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes]
rs6911272	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7738665	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741127	0.82[AMR][1000 genomes]
rs7760373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770443	0.84[EUR][1000 genomes]
rs875274	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9368811	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799298	chr6:34317120-34322841	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56330729	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34285200-34330600	Weak transcription	Thymus	Thymus
3	chr6:34285800-34326600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:34289000-34325200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:34298600-34326400	Weak transcription	A549	lung
6	chr6:34306000-34327800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:34306000-34328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:34308800-34330800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:34309600-34329200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:34309800-34321400	Weak transcription	Lung	lung
11	chr6:34309800-34327000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:34309800-34329800	Weak transcription	Fetal Thymus	thymus
13	chr6:34309800-34330800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:34309800-34337600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:34309800-34347200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:34310000-34330600	Weak transcription	Dnd41	blood
17	chr6:34310400-34321600	Weak transcription	Right Ventricle	heart
18	chr6:34310400-34329200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:34310600-34326400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:34310800-34330800	Weak transcription	Primary T cells from cord blood	blood
21	chr6:34311200-34321800	Weak transcription	Psoas Muscle	Psoas
22	chr6:34315400-34351200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:34316200-34333400	Weak transcription	Placenta	Placenta
24	chr6:34317400-34330800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:34318200-34326400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:34318200-34330600	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:34318200-34355800	Weak transcription	Brain Germinal Matrix	brain
28	chr6:34318400-34326000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:34318400-34330000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:34318600-34330600	Weak transcription	Fetal Intestine Small	intestine
31	chr6:34318800-34323600	Weak transcription	Brain Substantia Nigra	brain
32	chr6:34318800-34325600	Weak transcription	Fetal Heart	heart
33	chr6:34318800-34325800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:34318800-34327400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:34318800-34330600	Weak transcription	Adipose Nuclei	Adipose
36	chr6:34319400-34327600	Weak transcription	Right Atrium	heart
37	chr6:34319800-34321200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:34319800-34321400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:34320000-34321600	Enhancers	GM12878-XiMat	blood
40	chr6:34320000-34324000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:34320200-34321200	Enhancers	Brain Anterior Caudate	brain
42	chr6:34320200-34322200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:34320200-34324000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr6:34320200-34327600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:34320200-34330800	Weak transcription	Primary B cells from cord blood	blood
46	chr6:34320400-34321200	Weak transcription	Spleen	Spleen
47	chr6:34320400-34321200	Weak transcription	K562	blood
48	chr6:34320400-34321400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:34320400-34321400	Weak transcription	Left Ventricle	heart
50	chr6:34320400-34325800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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