Variant report

Variant	rs3754399
Chromosome Location	chr1:226869367-226869368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226864917..226866884-chr1:226868100..226871098,3	K562	blood:
2	chr1:226864917..226867492-chr1:226868629..226873346,4	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12095028	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846351	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16846357	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846378	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16846409	1.00[AFR][1000 genomes]
rs3754398	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754401	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754402	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754406	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754407	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
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[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3820647	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4653461	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4653464	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
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:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226864200-226871600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:226865600-226878000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:226866200-226870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:226866400-226874800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:226866800-226874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:226867000-226871800	Weak transcription	Dnd41	blood
7	chr1:226867600-226870000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:226867800-226874200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:226868000-226869400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:226868000-226870000	Weak transcription	Esophagus	oesophagus
11	chr1:226868000-226876000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:226868200-226869400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:226868200-226869400	Enhancers	Right Ventricle	heart
14	chr1:226868200-226870000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:226868200-226870000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:226868200-226870200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:226868200-226870400	Enhancers	Fetal Stomach	stomach
18	chr1:226868200-226870600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:226868200-226870800	Weak transcription	Gastric	stomach
20	chr1:226868200-226871000	Enhancers	Primary B cells from peripheral blood	blood
21	chr1:226868200-226871000	Enhancers	Placenta	Placenta
22	chr1:226868200-226871000	Enhancers	Lung	lung
23	chr1:226868200-226871600	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:226868200-226872000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:226868200-226873400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:226868200-226877400	Enhancers	Left Ventricle	heart
27	chr1:226868200-226884600	Enhancers	Brain Substantia Nigra	brain
28	chr1:226868400-226870000	Enhancers	Fetal Brain Female	brain
29	chr1:226868400-226870400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:226868400-226870600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:226868400-226870800	Enhancers	Right Atrium	heart
32	chr1:226868400-226872000	Genic enhancers	Primary T cells from cord blood	blood
33	chr1:226868400-226872200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:226868400-226872200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:226868400-226873200	Enhancers	Spleen	Spleen
36	chr1:226868400-226874200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:226868400-226876000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:226868400-226876800	Genic enhancers	Fetal Thymus	thymus
39	chr1:226868400-226876800	Genic enhancers	Thymus	Thymus
40	chr1:226868400-226877400	Enhancers	Psoas Muscle	Psoas
41	chr1:226868400-226880600	Enhancers	Brain Anterior Caudate	brain
42	chr1:226868400-226881200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:226868400-226881400	Enhancers	Brain Angular Gyrus	brain
44	chr1:226868400-226881800	Enhancers	Fetal Muscle Leg	muscle
45	chr1:226868600-226869400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
46	chr1:226868600-226869400	Weak transcription	Stomach Mucosa	stomach
47	chr1:226868600-226869600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
48	chr1:226868600-226869600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr1:226868600-226869600	Weak transcription	Fetal Brain Male	brain
50	chr1:226868600-226870000	Weak transcription	Rectal Mucosa Donor 31	rectum

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