Variant report

Variant	rs3754407
Chromosome Location	chr1:226879486-226879487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226849475..226852007-chr1:226878804..226881377,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12095028	1.00[ASN][1000 genomes]
rs16846351	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[ASN][1000 genomes]
rs16846357	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846378	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846409	1.00[AFR][1000 genomes]
rs16846452	0.86[AMR][1000 genomes]
rs16846458	0.86[AMR][1000 genomes]
rs16846461	0.86[AMR][1000 genomes]
rs16846464	0.86[AMR][1000 genomes]
rs3754398	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754399	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754401	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754403	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754406	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754409	1.00[ASW][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs3754413	1.00[ASW][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3754417	0.83[AMR][1000 genomes]
rs3768388	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768389	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768397	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768400	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768416	0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3820641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820647	0.88[CHB][hapmap];0.82[MEX][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs41440951	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs4653461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4653464	0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4653765	0.95[GIH][hapmap];0.82[MEX][hapmap]
rs4653766	0.95[GIH][hapmap]
rs56095953	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58091460	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7524854	0.93[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	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226868200-226884600	Enhancers	Brain Substantia Nigra	brain
2	chr1:226868400-226880600	Enhancers	Brain Anterior Caudate	brain
3	chr1:226868400-226881200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr1:226868400-226881400	Enhancers	Brain Angular Gyrus	brain
5	chr1:226868400-226881800	Enhancers	Fetal Muscle Leg	muscle
6	chr1:226868600-226881200	Enhancers	Adipose Nuclei	Adipose
7	chr1:226868600-226884800	Weak transcription	Fetal Kidney	kidney
8	chr1:226868600-226888200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:226869000-226880200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:226869000-226881800	Enhancers	Colon Smooth Muscle	Colon
11	chr1:226869000-226884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:226869000-226884200	Weak transcription	NHLF	lung
13	chr1:226869000-226884400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:226870000-226888800	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr1:226871000-226879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:226872000-226881000	Enhancers	Right Ventricle	heart
17	chr1:226872800-226890000	Weak transcription	Pancreas	Pancrea
18	chr1:226873400-226884600	Weak transcription	Gastric	stomach
19	chr1:226874200-226879800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:226874400-226880000	Enhancers	Brain Germinal Matrix	brain
21	chr1:226874400-226885200	Weak transcription	Colonic Mucosa	Colon
22	chr1:226874800-226880400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:226875200-226884600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:226876600-226884400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:226876600-226885000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:226876800-226881000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:226876800-226881200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr1:226876800-226881400	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:226876800-226884800	Weak transcription	HSMM	muscle
30	chr1:226876800-226887600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:226876800-226890400	Genic enhancers	Primary T cells from cord blood	blood
32	chr1:226877000-226879800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:226877000-226880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:226877000-226880600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:226877200-226881000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:226877200-226884600	Weak transcription	NHDF-Ad	bronchial
37	chr1:226877800-226879600	Enhancers	Aorta	Aorta
38	chr1:226877800-226881000	Enhancers	Left Ventricle	heart
39	chr1:226877800-226881200	Enhancers	Fetal Lung	lung
40	chr1:226877800-226881200	Enhancers	Placenta	Placenta
41	chr1:226877800-226881400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:226877800-226890200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:226878000-226879600	Enhancers	HUVEC	blood vessel
44	chr1:226878000-226879800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr1:226878000-226880000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:226878000-226880400	Enhancers	Lung	lung
47	chr1:226878000-226880800	Enhancers	Primary hematopoietic stem cells	blood
48	chr1:226878000-226880800	Genic enhancers	Fetal Thymus	thymus
49	chr1:226878000-226881000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr1:226878000-226881200	Enhancers	Fetal Muscle Trunk	muscle

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