Variant report

Variant	rs6429600
Chromosome Location	chr1:46864511-46864512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46862967..46865890-chr1:46874539..46876309,3	K562	blood:
2	chr1:46843998..46846044-chr1:46862468..46865325,2	K562	blood:
3	chr1:46859776..46861502-chr1:46863907..46865966,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489770	0.84[JPT][hapmap]
rs11590411	0.83[AMR][1000 genomes]
rs12029329	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]
rs1571138	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2145408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295632	0.88[EUR][1000 genomes]
rs2295633	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs324418	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs324420	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35361357	0.86[EUR][1000 genomes]
rs4660346	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4660928	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6670926	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6678149	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6699322	0.88[EUR][1000 genomes]
rs7555240	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
rs6429600	NSUN4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46860600-46864800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:46860600-46865800	Weak transcription	Small Intestine	intestine
3	chr1:46860600-46867200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:46861000-46865000	Weak transcription	Right Ventricle	heart
5	chr1:46861000-46874400	Weak transcription	Primary T cells from cord blood	blood
6	chr1:46861200-46864800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:46861200-46866200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:46861200-46867200	Weak transcription	Lung	lung
9	chr1:46861200-46867200	Weak transcription	Spleen	Spleen
10	chr1:46861200-46872200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:46861200-46879000	Weak transcription	Aorta	Aorta
12	chr1:46861200-46879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:46861400-46866000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:46861400-46866000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:46861400-46866000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:46861400-46866000	Weak transcription	Fetal Intestine Small	intestine
17	chr1:46861400-46866200	Weak transcription	Thymus	Thymus
18	chr1:46861400-46867200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:46861400-46867200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:46861400-46867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:46861400-46867400	Weak transcription	Psoas Muscle	Psoas
22	chr1:46861400-46867600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:46861600-46880400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:46861800-46867000	Weak transcription	Esophagus	oesophagus
25	chr1:46862000-46864600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:46862000-46864800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr1:46862000-46867200	Weak transcription	Adipose Nuclei	Adipose
28	chr1:46862200-46864800	Weak transcription	Fetal Thymus	thymus
29	chr1:46862200-46866000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:46862200-46866000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:46862200-46867600	Weak transcription	Left Ventricle	heart
32	chr1:46862200-46867600	Weak transcription	Ovary	ovary
33	chr1:46862400-46864800	Weak transcription	Brain Germinal Matrix	brain
34	chr1:46862400-46867600	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:46862400-46867600	Weak transcription	Fetal Brain Female	brain
36	chr1:46862800-46866000	Weak transcription	Colonic Mucosa	Colon
37	chr1:46863000-46864600	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:46863000-46864600	Weak transcription	Fetal Heart	heart
39	chr1:46863000-46864800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:46863000-46864800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:46863000-46865000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:46863000-46865800	Weak transcription	Brain Anterior Caudate	brain
43	chr1:46863000-46866000	Weak transcription	Fetal Intestine Large	intestine
44	chr1:46863000-46866000	Weak transcription	Pancreas	Pancrea
45	chr1:46863000-46866000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:46863000-46867000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:46863000-46867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:46863000-46867000	Weak transcription	Liver	Liver
49	chr1:46863000-46867000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:46863000-46867200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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