Variant report

Variant	rs2055154
Chromosome Location	chr3:23250855-23250856
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	chr3:23243375..23248925-chr3:23249833..23255104,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233153	Chromatin interaction
ENSG00000182247	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1013460	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1027379	0.80[EUR][1000 genomes]
rs11708117	0.83[AFR][1000 genomes]
rs11708176	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11720461	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11920019	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12330262	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12330479	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12493361	0.80[EUR][1000 genomes]
rs12629848	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13080261	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13080401	0.87[ASN][1000 genomes]
rs13081371	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1552930	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17012812	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17012869	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1973400	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2172828	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34919006	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4241511	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858062	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858064	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858483	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858484	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858491	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858492	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59429714	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6550746	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6550748	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6784771	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795492	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6804123	0.80[EUR][1000 genomes]
rs7429470	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617072	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7622784	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9310715	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9809176	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9816895	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9821101	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9826877	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836787	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9841123	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9841944	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9846398	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9847027	0.80[EUR][1000 genomes]
rs9848077	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9849176	0.80[EUR][1000 genomes]
rs9854148	0.80[EUR][1000 genomes]
rs9854590	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9861803	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9864908	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9865602	0.82[ASN][1000 genomes]
rs9874822	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999882	chr3:23121533-23257718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23245600-23251400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:23245600-23253400	Weak transcription	Lung	lung
3	chr3:23245800-23253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:23246000-23253000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:23246000-23260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:23246200-23251200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:23246200-23251200	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:23246200-23251200	Weak transcription	Psoas Muscle	Psoas
10	chr3:23246200-23252200	Weak transcription	Fetal Stomach	stomach
11	chr3:23246200-23257200	Weak transcription	Ovary	ovary
12	chr3:23246200-23257400	Weak transcription	Left Ventricle	heart
13	chr3:23246200-23258800	Weak transcription	HSMM	muscle
14	chr3:23246200-23259000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:23246200-23259000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:23246200-23259200	Weak transcription	NH-A	brain
17	chr3:23246200-23260600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:23246400-23251000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:23246400-23251400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:23246400-23253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:23246400-23259400	Weak transcription	Osteobl	bone
23	chr3:23246400-23261200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
25	chr3:23246600-23251200	Weak transcription	Adipose Nuclei	Adipose
26	chr3:23246600-23251200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:23246600-23251200	Weak transcription	HMEC	breast
28	chr3:23246600-23251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:23246600-23252800	Weak transcription	HUVEC	blood vessel
30	chr3:23246600-23254800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:23246600-23258800	Weak transcription	Fetal Lung	lung
32	chr3:23246600-23259000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:23246600-23259000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:23246600-23259200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:23246600-23259200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:23246600-23260000	Weak transcription	NHEK	skin
37	chr3:23246600-23260800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:23246800-23251200	Weak transcription	Liver	Liver
40	chr3:23246800-23252200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:23246800-23259000	Weak transcription	NHLF	lung
42	chr3:23246800-23259800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:23247400-23258400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:23248200-23258400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:23248200-23259000	Weak transcription	A549	lung
46	chr3:23248200-23260600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:23248400-23251400	Weak transcription	Primary B cells from cord blood	blood
48	chr3:23248800-23251200	Weak transcription	Thymus	Thymus
49	chr3:23248800-23257200	Weak transcription	Brain Angular Gyrus	brain
50	chr3:23248800-23257400	Weak transcription	Brain Substantia Nigra	brain

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