Variant report

Variant	rs41440951
Chromosome Location	chr1:226842299-226842300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226841357..226843644-chr1:226846781..226848599,2	MCF-7	breast:
2	chr1:226841585..226843575-chr1:226849581..226851350,2	MCF-7	breast:
3	chr1:226834023..226836698-chr1:226841817..226845290,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16846351	1.00[ASW][hapmap];0.85[MEX][hapmap]
rs16846378	1.00[MEX][hapmap]
rs17589895	1.00[YRI][hapmap]
rs3754388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754406	0.86[CHB][hapmap]
rs3754407	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs3754409	1.00[ASW][hapmap];0.82[MEX][hapmap]
rs3754413	1.00[ASW][hapmap]
rs3768393	1.00[YRI][hapmap]
rs3820640	1.00[YRI][hapmap]
rs3820647	0.82[MEX][hapmap]
rs41268731	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4653456	0.86[EUR][1000 genomes]
rs4653458	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653460	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653760	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4653761	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653765	0.82[MEX][hapmap]
rs73098900	0.86[EUR][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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	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
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226829400-226843800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:226832000-226843800	Weak transcription	HMEC	breast
3	chr1:226832400-226843600	Weak transcription	Stomach Mucosa	stomach
4	chr1:226833600-226844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:226836000-226844000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:226836000-226844200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:226836400-226847200	Weak transcription	Ovary	ovary
8	chr1:226836800-226856200	Enhancers	Left Ventricle	heart
9	chr1:226837000-226843800	Enhancers	Colon Smooth Muscle	Colon
10	chr1:226837000-226849800	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr1:226837200-226843000	Enhancers	Brain Hippocampus Middle	brain
12	chr1:226837200-226844800	Enhancers	Right Ventricle	heart
13	chr1:226837200-226846000	Enhancers	Brain Anterior Caudate	brain
14	chr1:226837400-226842400	Weak transcription	Gastric	stomach
15	chr1:226837400-226843800	Weak transcription	Fetal Brain Male	brain
16	chr1:226837400-226844000	Weak transcription	NHEK	skin
17	chr1:226837400-226848600	Enhancers	Right Atrium	heart
18	chr1:226837400-226856200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:226837400-226856600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:226837400-226856600	Enhancers	Brain Substantia Nigra	brain
21	chr1:226837600-226844600	Enhancers	Placenta	Placenta
22	chr1:226837600-226845600	Enhancers	Lung	lung
23	chr1:226837800-226844400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:226838200-226845200	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:226838800-226848200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:226839200-226846800	Enhancers	Spleen	Spleen
27	chr1:226839400-226845400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:226839400-226856200	Enhancers	Fetal Muscle Leg	muscle
29	chr1:226839600-226843600	Enhancers	Primary B cells from cord blood	blood
30	chr1:226839800-226844800	Genic enhancers	Fetal Stomach	stomach
31	chr1:226840000-226843800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:226840000-226846200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:226840200-226845600	Weak transcription	Aorta	Aorta
34	chr1:226840400-226844000	Enhancers	Stomach Smooth Muscle	stomach
35	chr1:226840400-226846000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:226840600-226842400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:226840600-226843000	Enhancers	Small Intestine	intestine
38	chr1:226840600-226843400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:226840600-226845000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr1:226840600-226851800	Enhancers	Adipose Nuclei	Adipose
41	chr1:226840600-226852600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:226840600-226852800	Enhancers	Primary hematopoietic stem cells	blood
43	chr1:226840800-226843800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr1:226840800-226844200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:226840800-226844800	Enhancers	Colonic Mucosa	Colon
46	chr1:226840800-226845200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:226840800-226845400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr1:226840800-226845600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:226841000-226842400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr1:226841000-226842400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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