Variant report

Variant	rs3754413
Chromosome Location	chr1:226924196-226924197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1124377	0.83[AMR][1000 genomes]
rs12072939	0.80[AMR][1000 genomes]
rs12095028	0.82[ASN][1000 genomes]
rs16846351	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs16846357	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16846378	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16846413	1.00[AFR][1000 genomes]
rs16846452	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846458	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846461	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846464	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs16846466	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3754398	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754399	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754400	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754401	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754402	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754403	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754406	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754407	1.00[ASW][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754409	1.00[ASW][hapmap]
rs3754417	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3768388	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768389	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768397	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768400	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768416	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820641	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3820647	0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41440951	1.00[ASW][hapmap]
rs4653461	0.82[ASN][1000 genomes]
rs4653464	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653763	1.00[AFR][1000 genomes]
rs4653769	1.00[JPT][hapmap]
rs56095953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58091460	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59173465	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs60932168	1.00[AFR][1000 genomes]
rs7524854	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv3338179	chr1:226923854-226926702	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226891800-226924800	Weak transcription	Aorta	Aorta
2	chr1:226909800-226924200	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr1:226910000-226925000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr1:226912400-226924600	Weak transcription	Ovary	ovary
5	chr1:226912800-226925400	Weak transcription	Stomach Mucosa	stomach
6	chr1:226915000-226925000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
7	chr1:226916800-226924200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:226918600-226925000	Transcr. at gene 5' and 3'	Thymus	Thymus
9	chr1:226918800-226925000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
10	chr1:226918800-226925800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:226919200-226924400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:226920000-226925200	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:226920400-226924200	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr1:226920400-226924400	Genic enhancers	Spleen	Spleen
15	chr1:226920400-226924600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:226920400-226924600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:226920400-226924600	Genic enhancers	Fetal Lung	lung
18	chr1:226920400-226924800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
19	chr1:226920400-226924800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr1:226920400-226925000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
21	chr1:226920400-226927000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
22	chr1:226920600-226924400	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:226920600-226924600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
24	chr1:226920600-226924800	Strong transcription	NHEK	skin
25	chr1:226920600-226925000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:226920600-226925000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:226920600-226925000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
28	chr1:226920800-226927200	Active TSS	Psoas Muscle	Psoas
29	chr1:226921000-226924800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:226921000-226927600	Active TSS	Right Atrium	heart
31	chr1:226921200-226924800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:226921600-226924600	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
33	chr1:226921600-226924600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
34	chr1:226921800-226924400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:226921800-226924400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
36	chr1:226921800-226924600	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
37	chr1:226922000-226924200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:226922000-226924800	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
39	chr1:226922200-226924200	Genic enhancers	NHLF	lung
40	chr1:226922200-226925000	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
41	chr1:226922400-226924800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr1:226922400-226925000	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
43	chr1:226922400-226925000	Enhancers	Liver	Liver
44	chr1:226922600-226924400	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr1:226922600-226924600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:226922600-226924600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
47	chr1:226922600-226924600	Weak transcription	HMEC	breast
48	chr1:226922600-226924600	Weak transcription	NHDF-Ad	bronchial
49	chr1:226922600-226924800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:226922600-226924800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle

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