Variant report

Variant	rs12029329
Chromosome Location	chr1:46879856-46879857
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46875600..46878461-chr1:46878712..46880340,2	K562	blood:
2	chr1:46877384..46880192-chr1:46886076..46889204,3	K562	blood:

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10489770	0.85[JPT][hapmap]
rs11590411	0.82[AMR][1000 genomes]
rs1571138	0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2145408	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295632	0.94[EUR][1000 genomes]
rs2295633	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs324418	0.83[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs324420	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35361357	0.92[EUR][1000 genomes]
rs4660346	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660928	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6429600	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6670926	0.87[CEU][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678149	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6699322	0.94[EUR][1000 genomes]
rs7555240	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	32 gene(s)	inside rSNPs	diseases
6	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12029329	NSUN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46861600-46880400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:46868000-46884200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:46868200-46883800	Weak transcription	HepG2	liver
4	chr1:46869000-46882000	Strong transcription	Fetal Intestine Small	intestine
5	chr1:46872200-46880200	Strong transcription	Pancreas	Pancrea
6	chr1:46872200-46884800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:46872600-46880400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:46872800-46880400	Strong transcription	Liver	Liver
9	chr1:46872800-46880400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:46872800-46880400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr1:46872800-46882400	Weak transcription	Ovary	ovary
12	chr1:46872800-46882400	Weak transcription	Right Ventricle	heart
13	chr1:46872800-46908000	Weak transcription	Right Atrium	heart
14	chr1:46873000-46880600	Strong transcription	Gastric	stomach
15	chr1:46873000-46880800	Weak transcription	Fetal Thymus	thymus
16	chr1:46873000-46881000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:46873200-46880000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:46873200-46880000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:46873400-46880000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:46873600-46880000	Strong transcription	Thymus	Thymus
21	chr1:46873600-46880600	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:46873800-46880400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:46874200-46880200	Strong transcription	Brain Germinal Matrix	brain
24	chr1:46874200-46880200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:46874200-46881200	Strong transcription	Fetal Stomach	stomach
26	chr1:46874800-46881800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:46875000-46882000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:46875200-46887800	Weak transcription	Stomach Mucosa	stomach
29	chr1:46876000-46882600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:46877000-46884000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:46877400-46884800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:46878000-46880400	Strong transcription	Fetal Brain Female	brain
33	chr1:46878400-46880000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:46878600-46880000	Strong transcription	Adipose Nuclei	Adipose
35	chr1:46878600-46880400	Strong transcription	Esophagus	oesophagus
36	chr1:46878800-46880000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:46878800-46880200	Strong transcription	Lung	lung
38	chr1:46878800-46880200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:46878800-46880400	Strong transcription	Fetal Intestine Large	intestine
40	chr1:46878800-46882600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:46879000-46880200	Strong transcription	Aorta	Aorta
42	chr1:46879000-46881200	Strong transcription	Colonic Mucosa	Colon
43	chr1:46879000-46881400	Weak transcription	Brain Angular Gyrus	brain
44	chr1:46879000-46881800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:46879000-46882000	Strong transcription	Brain Anterior Caudate	brain
46	chr1:46879000-46886400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:46879200-46880000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:46879200-46880400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:46879200-46880400	Enhancers	K562	blood
50	chr1:46879200-46881600	Weak transcription	Fetal Muscle Leg	muscle

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