Variant report

Variant	rs3798554
Chromosome Location	chr6:34268684-34268685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34204531..34206261-chr6:34268326..34273116,4	K562	blood:
2	chr6:34266980..34269551-chr6:34289025..34290920,2	K562	blood:
3	chr4:144552998..144554498-chr6:34268238..34270073,2	K562	blood:
4	chr6:34263488..34269053-chr6:34269608..34275567,7	K562	blood:

Variant related genes	Relation type
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10484267	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10484268	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1057691	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1060308	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10648	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1127084	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1265	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12654	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13466	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16883137	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16883475	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16883896	0.80[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16888452	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17628798	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17628946	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17629180	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17629270	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17696583	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17696774	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17696829	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1994923	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs206922	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3798557	0.80[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41269032	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41269034	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41269036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41269038	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713771	0.83[EUR][1000 genomes]
rs55674397	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55684754	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55694290	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55763242	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55779010	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55798596	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55812200	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55833185	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55863933	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55864834	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56033036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56039915	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56107559	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56188036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56274913	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56309550	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56323997	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56330729	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59832183	0.84[AMR][1000 genomes]
rs62399870	0.83[EUR][1000 genomes]
rs6911272	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7738665	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760373	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7770443	0.80[EUR][1000 genomes]
rs875274	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9368811	0.82[AMR][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
rs3798554	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:34253600-34271200	Weak transcription	Stomach Mucosa	stomach
5	chr6:34260200-34272800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:34261400-34269000	Weak transcription	NHDF-Ad	bronchial
7	chr6:34261400-34269200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:34261400-34269400	Weak transcription	NHLF	lung
9	chr6:34261400-34273400	Weak transcription	Fetal Kidney	kidney
10	chr6:34261400-34276000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:34261600-34269200	Weak transcription	NH-A	brain
12	chr6:34261600-34269200	Weak transcription	Osteobl	bone
13	chr6:34261600-34273400	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:34261600-34276200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:34261800-34269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:34261800-34269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:34261800-34269200	Weak transcription	Brain Germinal Matrix	brain
18	chr6:34261800-34269400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:34261800-34271200	Weak transcription	HUVEC	blood vessel
20	chr6:34261800-34273600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:34261800-34275200	Weak transcription	Aorta	Aorta
22	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:34262000-34269000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:34262000-34269000	Weak transcription	Brain Angular Gyrus	brain
25	chr6:34262000-34269000	Weak transcription	Fetal Lung	lung
26	chr6:34262000-34269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:34262000-34269200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:34262000-34269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:34262000-34269200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr6:34262000-34269200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:34262000-34269400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:34262000-34274000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:34262000-34276800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:34262000-34282600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:34262000-34282800	Weak transcription	Primary T cells from cord blood	blood
36	chr6:34262000-34283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:34262000-34284600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:34262000-34286600	Weak transcription	Gastric	stomach
39	chr6:34262000-34289000	Weak transcription	Hela-S3	cervix
40	chr6:34262000-34292800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:34262200-34269200	Weak transcription	Adipose Nuclei	Adipose
42	chr6:34262200-34269200	Weak transcription	Ovary	ovary
43	chr6:34262200-34269400	Weak transcription	Liver	Liver
44	chr6:34262200-34273400	Weak transcription	Fetal Brain Female	brain
45	chr6:34262200-34276000	Weak transcription	Pancreas	Pancrea
46	chr6:34262200-34295400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:34262200-34301200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:34262800-34269000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:34262800-34272000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:34262800-34290800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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