Variant report

Variant	rs3798556
Chromosome Location	chr6:34294006-34294007
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34209691..34211647-chr6:34293997..34295564,2	K562	blood:
2	chr6:34292790..34296171-chr6:34350622..34353853,3	K562	blood:
3	chr6:34292928..34295452-chr6:34306774..34308338,2	K562	blood:
4	chr6:34283435..34288525-chr6:34290742..34294904,6	K562	blood:
5	chr6:34286471..34290477-chr6:34292697..34296631,5	K562	blood:
6	chr6:34288743..34290289-chr6:34292325..34294545,2	K562	blood:
7	chr6:34204010..34208020-chr6:34292520..34295765,4	K562	blood:
8	chr6:34273952..34276899-chr6:34292317..34294355,2	K562	blood:
9	chr6:34239719..34243509-chr6:34291067..34294837,5	K562	blood:
10	chr6:34292426..34294070-chr6:34358981..34360614,2	K562	blood:
11	chr6:34211075..34213975-chr6:34293539..34295435,2	K562	blood:
12	chr6:34292426..34294202-chr6:34358890..34360481,2	K562	blood:
13	chr6:34201303..34203546-chr6:34292849..34294793,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs169584	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1811968	0.83[EUR][1000 genomes]
rs2006833	0.85[EUR][1000 genomes]
rs206919	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs206920	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs206921	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs206924	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs206936	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs206941	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs206942	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237098	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798560	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3913009	0.84[EUR][1000 genomes]
rs3913010	0.84[EUR][1000 genomes]
rs410340	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs414739	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs458576	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4587164	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs464553	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs568502	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57622072	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62399909	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6457773	0.80[EUR][1000 genomes]
rs6907486	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6912971	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6924482	0.83[EUR][1000 genomes]
rs6924682	0.85[ASN][1000 genomes]
rs6924982	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930978	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7752035	0.86[ASN][1000 genomes]
rs7757586	0.83[EUR][1000 genomes]
rs7757900	0.84[EUR][1000 genomes]
rs7765498	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368813	0.84[EUR][1000 genomes]
rs9380433	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9394214	0.85[EUR][1000 genomes]
rs9394215	0.83[EUR][1000 genomes]
rs9461981	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9469775	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9469779	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv1794528	chr6:34267024-34308816	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798556	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 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	chr6:34262200-34295400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:34262200-34301200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:34264000-34299000	Weak transcription	Dnd41	blood
5	chr6:34274400-34306400	Weak transcription	Brain Germinal Matrix	brain
6	chr6:34274400-34309000	Weak transcription	NHDF-Ad	bronchial
7	chr6:34275200-34298000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:34275800-34299600	Weak transcription	Lung	lung
9	chr6:34280800-34295600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:34284000-34301600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:34284000-34308200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:34284600-34300400	Weak transcription	Primary T cells from cord blood	blood
13	chr6:34284800-34299000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:34284800-34310800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:34285000-34305600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:34285200-34330600	Weak transcription	Thymus	Thymus
17	chr6:34285400-34299200	Weak transcription	HSMM	muscle
18	chr6:34285400-34305200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:34285400-34305400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:34285400-34307800	Weak transcription	Liver	Liver
21	chr6:34285800-34308800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:34285800-34326600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:34286000-34308200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:34286600-34302800	Weak transcription	Osteobl	bone
25	chr6:34287000-34298000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:34287000-34299400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:34287000-34301200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:34287000-34305000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:34287200-34299000	Weak transcription	Primary B cells from cord blood	blood
30	chr6:34287200-34299400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:34287400-34297800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:34287400-34299200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:34287400-34299400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:34287400-34300400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:34287400-34300800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:34287400-34300800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:34287400-34301600	Weak transcription	Spleen	Spleen
38	chr6:34287400-34304000	Weak transcription	Colonic Mucosa	Colon
39	chr6:34287600-34299200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:34287600-34299400	Weak transcription	GM12878-XiMat	blood
41	chr6:34287600-34305400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:34287600-34305400	Weak transcription	Right Atrium	heart
43	chr6:34287600-34306400	Weak transcription	Fetal Lung	lung
44	chr6:34287600-34309200	Weak transcription	Pancreas	Pancrea
45	chr6:34287800-34299600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:34288000-34299200	Weak transcription	HepG2	liver
47	chr6:34288600-34298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:34289000-34294600	Weak transcription	Fetal Intestine Small	intestine
49	chr6:34289000-34325200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:34289400-34308200	Weak transcription	Fetal Intestine Large	intestine

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