Variant report

Variant	rs2047409
Chromosome Location	chr4:106137033-106137034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10007915	0.80[AMR][1000 genomes]
rs1032625	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10461139	0.92[ASN][1000 genomes]
rs11097882	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11721948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11726786	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11735256	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639764	0.82[ASN][1000 genomes]
rs12645144	0.94[ASN][1000 genomes]
rs13103161	0.82[ASN][1000 genomes]
rs13109676	0.90[ASN][1000 genomes]
rs13147502	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1391438	0.80[CEU][hapmap]
rs1391439	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1391441	0.80[CEU][hapmap]
rs2007403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454205	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2454206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2647244	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2647250	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs2647251	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2647257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2647268	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2726459	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2726460	0.94[ASN][1000 genomes]
rs2726491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2726519	0.92[ASN][1000 genomes]
rs2726520	0.92[ASN][1000 genomes]
rs2726521	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34104813	0.93[ASN][1000 genomes]
rs4699165	0.94[ASN][1000 genomes]
rs55838312	0.95[ASN][1000 genomes]
rs62330911	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs62331159	0.97[ASN][1000 genomes]
rs62332760	0.97[ASN][1000 genomes]
rs62332762	0.82[ASN][1000 genomes]
rs6533183	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6818637	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6839705	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6855629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7655890	0.80[CEU][hapmap]
rs7658539	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7663401	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7670522	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs7674220	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7683416	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2047409	NPNT	cis	Lymphoblastoid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
2	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:106113000-106154800	Weak transcription	Fetal Thymus	thymus
4	chr4:106113200-106146600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:106114400-106155200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:106114600-106145400	Weak transcription	Adipose Nuclei	Adipose
9	chr4:106114600-106155600	Weak transcription	Esophagus	oesophagus
10	chr4:106118000-106155400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:106118800-106155000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:106118800-106155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:106122200-106137200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:106127600-106146600	Weak transcription	Left Ventricle	heart
15	chr4:106127600-106155000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:106127600-106155400	Weak transcription	Placenta	Placenta
17	chr4:106127800-106144800	Weak transcription	Ovary	ovary
18	chr4:106127800-106145200	Weak transcription	Fetal Heart	heart
19	chr4:106127800-106155200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:106127800-106155200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:106128000-106154000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:106128200-106138200	Weak transcription	Brain Germinal Matrix	brain
23	chr4:106131200-106138200	Weak transcription	Primary B cells from cord blood	blood
24	chr4:106131800-106155000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:106132000-106153200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:106132400-106144800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:106132400-106146600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:106132400-106154600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:106132800-106141600	Weak transcription	Small Intestine	intestine
30	chr4:106133400-106155000	Weak transcription	Fetal Lung	lung
31	chr4:106133800-106155000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:106135200-106155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:106135200-106155000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr4:106135600-106137800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:106135600-106137800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:106135800-106137600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:106135800-106137600	Enhancers	HSMM	muscle
38	chr4:106135800-106137600	Enhancers	NHEK	skin
39	chr4:106135800-106138200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:106135800-106146600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:106136000-106137400	Enhancers	Brain Substantia Nigra	brain
42	chr4:106136000-106137600	Enhancers	Brain Anterior Caudate	brain
43	chr4:106136000-106138400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr4:106136000-106145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:106136000-106155000	Weak transcription	Fetal Stomach	stomach
46	chr4:106136000-106157400	Weak transcription	Right Ventricle	heart
47	chr4:106136200-106137600	Enhancers	Fetal Intestine Small	intestine
48	chr4:106136200-106138400	Enhancers	Brain Hippocampus Middle	brain
49	chr4:106136200-106146600	Weak transcription	Psoas Muscle	Psoas
50	chr4:106136400-106137600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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