Variant report

Variant	rs949840
Chromosome Location	chr1:221065371-221065372
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221059069..221061749-chr1:221063321..221065597,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs2050525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484697	0.81[EUR][1000 genomes]
rs2738750	0.84[AFR][1000 genomes]
rs2784251	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2784253	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784255	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2784270	0.81[EUR][1000 genomes]
rs2784271	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2784272	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2784274	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2807859	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2807860	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2807863	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2807864	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2807865	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2807867	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2807869	0.81[EUR][1000 genomes]
rs867027	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945448	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs949839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1798350	chr1:221020278-221069740	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221062000-221065600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:221062200-221066200	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:221064000-221067000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr1:221064200-221065600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:221064400-221065400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
6	chr1:221064400-221065400	Bivalent Enhancer	HUVEC	blood vessel
7	chr1:221064400-221065600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:221064400-221065600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr1:221064400-221067600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:221064600-221065400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr1:221064600-221065400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
12	chr1:221064600-221065400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:221064600-221065400	Bivalent Enhancer	Brain Hippocampus Middle	brain
14	chr1:221064600-221065400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr1:221064600-221065600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
16	chr1:221064600-221065600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
17	chr1:221064600-221065600	Enhancers	Pancreas	Pancrea
18	chr1:221064600-221065600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr1:221064600-221065600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
20	chr1:221064600-221065600	ZNF genes & repeats	Spleen	Spleen
21	chr1:221064600-221065800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr1:221064800-221065400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:221064800-221065400	Bivalent Enhancer	Liver	Liver
24	chr1:221064800-221065400	Bivalent Enhancer	Fetal Brain Male	brain
25	chr1:221064800-221065600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:221064800-221065600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:221065000-221065400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:221065000-221065600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:221065000-221065600	Bivalent Enhancer	Fetal Stomach	stomach
30	chr1:221065000-221065600	ZNF genes & repeats	Right Atrium	heart
31	chr1:221065200-221065400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:221065200-221065400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:221065200-221065400	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr1:221065200-221065400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
35	chr1:221065200-221065400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
36	chr1:221065200-221065600	Bivalent Enhancer	Left Ventricle	heart
37	chr1:221065200-221065600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr1:221065200-221066200	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr1:221065200-221066800	Weak transcription	Right Ventricle	heart
40	chr1:221065200-221067000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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