Variant report

Variant	rs2789910
Chromosome Location	chr1:223173030-223173031
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223168965..223171171-chr1:223172792..223175286,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11487819	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2378617	0.80[EUR][1000 genomes]
rs2378618	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2378619	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609359	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2609366	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2609371	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2789924	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789929	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789931	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789933	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2789934	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2789937	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2789945	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2789953	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789954	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2789957	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2789958	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2789972	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34188904	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34620158	0.85[AMR][1000 genomes]
rs34673329	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4317816	0.90[AMR][1000 genomes]
rs4509582	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4846783	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61837491	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67420224	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs728006	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946506	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv917330	chr1:223141547-223225893	Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223147000-223175800	Weak transcription	Aorta	Aorta
2	chr1:223148200-223175600	Weak transcription	Fetal Stomach	stomach
3	chr1:223149800-223175600	Weak transcription	Ovary	ovary
4	chr1:223150200-223173600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:223152400-223175600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:223153200-223175600	Weak transcription	Esophagus	oesophagus
7	chr1:223155200-223175800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:223156000-223175800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:223156600-223175800	Weak transcription	Spleen	Spleen
10	chr1:223157800-223175800	Weak transcription	Gastric	stomach
11	chr1:223158200-223175800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:223158800-223175800	Weak transcription	Placenta	Placenta
13	chr1:223158800-223175800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:223160200-223175600	Weak transcription	Thymus	Thymus
15	chr1:223163600-223179800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:223163800-223175600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:223164000-223175800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:223165000-223175800	Weak transcription	Fetal Brain Male	brain
19	chr1:223165600-223176000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:223166200-223179400	Weak transcription	Small Intestine	intestine
21	chr1:223166800-223175000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:223167000-223175000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:223167000-223176000	Weak transcription	Brain Angular Gyrus	brain
24	chr1:223167200-223175600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:223167200-223176200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:223167800-223175800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:223168400-223175800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:223168600-223175800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:223168800-223173600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:223168800-223175600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:223168800-223175600	Weak transcription	Pancreas	Pancrea
32	chr1:223168800-223175800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:223169000-223173400	Weak transcription	Liver	Liver
34	chr1:223169000-223173600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:223169000-223173800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:223169000-223175000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:223169000-223175000	Weak transcription	NHDF-Ad	bronchial
38	chr1:223169000-223175600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:223169000-223175600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:223169000-223175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:223169000-223175600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:223169000-223175600	Weak transcription	Lung	lung
43	chr1:223169000-223175600	Weak transcription	Right Ventricle	heart
44	chr1:223169000-223175600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:223169000-223175800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:223169000-223175800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:223169000-223175800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:223169000-223175800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:223169000-223176000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:223169000-223177200	Weak transcription	Muscle Satellite Cultured Cells	--

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