Variant report

Variant	rs2145408
Chromosome Location	chr1:46861907-46861908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46851709..46853903-chr1:46860122..46862879,2	K562	blood:
2	chr1:46861085..46863175-chr1:46866274..46868235,2	K562	blood:
3	chr1:46860730..46862253-chr1:46871679..46874541,2	K562	blood:

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10489770	0.86[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap]
rs11590411	0.86[AMR][1000 genomes]
rs12029329	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]
rs1547180	0.86[ASW][hapmap]
rs1571138	0.93[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2295632	0.87[EUR][1000 genomes]
rs2295633	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs324418	0.93[ASW][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs324420	1.00[ASW][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35361357	0.85[EUR][1000 genomes]
rs4660346	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4660928	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6429600	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]
rs6670926	0.81[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6678149	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6689182	0.87[MEX][hapmap]
rs6699322	0.87[EUR][1000 genomes]
rs7555240	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2145408	MMACHC	cis	cerebellum	SCAN
rs2145408	NSUN4	cis	lymphoblastoid	seeQTL

Chromatin state (count:64 , 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	chr1:46860800-46862200	Enhancers	Ovary	ovary
5	chr1:46860800-46862800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:46860800-46863000	Enhancers	Fetal Lung	lung
7	chr1:46860800-46863000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:46860800-46863000	Enhancers	Right Atrium	heart
9	chr1:46860800-46863200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr1:46861000-46863000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:46861000-46863000	Enhancers	Pancreas	Pancrea
12	chr1:46861000-46865000	Weak transcription	Right Ventricle	heart
13	chr1:46861000-46874400	Weak transcription	Primary T cells from cord blood	blood
14	chr1:46861200-46862000	Enhancers	Adipose Nuclei	Adipose
15	chr1:46861200-46862000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:46861200-46862200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:46861200-46862400	Enhancers	Brain Germinal Matrix	brain
18	chr1:46861200-46862800	Enhancers	Colonic Mucosa	Colon
19	chr1:46861200-46863000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:46861200-46863000	Enhancers	Gastric	stomach
21	chr1:46861200-46863000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:46861200-46863200	Enhancers	Stomach Mucosa	stomach
23	chr1:46861200-46863200	Enhancers	NHEK	skin
24	chr1:46861200-46864800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:46861200-46866200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:46861200-46867200	Weak transcription	Lung	lung
27	chr1:46861200-46867200	Weak transcription	Spleen	Spleen
28	chr1:46861200-46872200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:46861200-46879000	Weak transcription	Aorta	Aorta
30	chr1:46861200-46879400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:46861400-46862200	Enhancers	Brain Hippocampus Middle	brain
32	chr1:46861400-46862200	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:46861400-46862200	Enhancers	Fetal Intestine Large	intestine
34	chr1:46861400-46862200	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:46861400-46862400	Enhancers	Fetal Brain Female	brain
36	chr1:46861400-46863000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:46861400-46863000	Enhancers	Liver	Liver
38	chr1:46861400-46863000	Enhancers	Brain Angular Gyrus	brain
39	chr1:46861400-46863000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:46861400-46863000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:46861400-46863200	Enhancers	Brain Substantia Nigra	brain
42	chr1:46861400-46866000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:46861400-46866000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:46861400-46866000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:46861400-46866000	Weak transcription	Fetal Intestine Small	intestine
46	chr1:46861400-46866200	Weak transcription	Thymus	Thymus
47	chr1:46861400-46867200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:46861400-46867200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:46861400-46867400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:46861400-46867400	Weak transcription	Psoas Muscle	Psoas

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