Variant report

Variant	rs3754402
Chromosome Location	chr1:226876363-226876364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226875941..226879287-chr1:226889966..226892608,3	MCF-7	breast:
2	chr1:226870709..226873469-chr1:226876259..226878342,2	K562	blood:
3	chr1:226871969..226874742-chr1:226876259..226878047,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12095028	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846351	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16846357	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846378	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754399	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754409	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3754413	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3768388	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768397	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768400	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3768416	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3820641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820647	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4653461	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653463	1.00[CHB][hapmap]
rs4653464	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4653765	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4653766	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs56095953	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58091460	1.00[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:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226865600-226878000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:226868200-226877400	Enhancers	Left Ventricle	heart
3	chr1:226868200-226884600	Enhancers	Brain Substantia Nigra	brain
4	chr1:226868400-226876800	Genic enhancers	Fetal Thymus	thymus
5	chr1:226868400-226876800	Genic enhancers	Thymus	Thymus
6	chr1:226868400-226877400	Enhancers	Psoas Muscle	Psoas
7	chr1:226868400-226880600	Enhancers	Brain Anterior Caudate	brain
8	chr1:226868400-226881200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:226868400-226881400	Enhancers	Brain Angular Gyrus	brain
10	chr1:226868400-226881800	Enhancers	Fetal Muscle Leg	muscle
11	chr1:226868600-226876400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:226868600-226877200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr1:226868600-226878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:226868600-226881200	Enhancers	Adipose Nuclei	Adipose
15	chr1:226868600-226884800	Weak transcription	Fetal Kidney	kidney
16	chr1:226868600-226888200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:226868800-226878000	Weak transcription	NHEK	skin
18	chr1:226869000-226878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:226869000-226880200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:226869000-226881800	Enhancers	Colon Smooth Muscle	Colon
21	chr1:226869000-226884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:226869000-226884200	Weak transcription	NHLF	lung
23	chr1:226869000-226884400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:226869400-226878000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:226869400-226878400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:226870000-226888800	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr1:226870400-226878200	Weak transcription	Stomach Mucosa	stomach
28	chr1:226871000-226878000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:226871000-226879600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:226871800-226877200	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:226871800-226877200	Enhancers	Right Atrium	heart
32	chr1:226871800-226878000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:226872000-226876400	Enhancers	Esophagus	oesophagus
34	chr1:226872000-226881000	Enhancers	Right Ventricle	heart
35	chr1:226872600-226878000	Weak transcription	Dnd41	blood
36	chr1:226872800-226876600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:226872800-226890000	Weak transcription	Pancreas	Pancrea
38	chr1:226873000-226877200	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:226873400-226876800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:226873400-226877200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:226873400-226884600	Weak transcription	Gastric	stomach
42	chr1:226873800-226877000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:226874000-226877000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:226874000-226877400	Enhancers	Placenta	Placenta
45	chr1:226874200-226876400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:226874200-226876400	Strong transcription	Fetal Intestine Small	intestine
47	chr1:226874200-226876400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:226874200-226877000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:226874200-226879800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:226874400-226876600	Enhancers	Primary hematopoietic stem cells	blood

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