Variant report

Variant	rs1552931
Chromosome Location	chr3:23248486-23248487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23247004..23248744-chr3:23272999..23274643,2	K562	blood:
2	chr3:23243580..23246628-chr3:23247045..23250539,6	MCF-7	breast:
3	chr3:23247857..23249626-chr3:23258764..23261200,2	MCF-7	breast:
4	chr3:23244971..23246744-chr3:23246760..23249188,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233153	Chromatin interaction
ENSG00000182247	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1027380	0.81[ASN][1000 genomes]
rs11711630	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11715107	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13087416	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13095887	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1390083	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1495133	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1495134	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17342342	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047340	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs2055155	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs2088129	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2132145	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2132147	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2132148	0.81[CEU][hapmap];0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2132149	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36073188	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4334589	0.91[ASN][1000 genomes]
rs4858065	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858066	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858488	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858498	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769959	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6790185	0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6799861	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6806387	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73149661	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618910	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7629327	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs7635882	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7648425	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs903519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs923996	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9826103	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9836135	0.80[AFR][1000 genomes]
rs9840015	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9844558	0.87[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9848331	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][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:69 , 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	chr3:23246200-23248600	Weak transcription	Fetal Heart	heart
8	chr3:23246200-23251200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:23246200-23251200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:23246200-23251200	Weak transcription	Psoas Muscle	Psoas
11	chr3:23246200-23252200	Weak transcription	Fetal Stomach	stomach
12	chr3:23246200-23257200	Weak transcription	Ovary	ovary
13	chr3:23246200-23257400	Weak transcription	Left Ventricle	heart
14	chr3:23246200-23258800	Weak transcription	HSMM	muscle
15	chr3:23246200-23259000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:23246200-23259000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:23246200-23259200	Weak transcription	NH-A	brain
18	chr3:23246200-23260600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:23246400-23250000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:23246400-23250800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:23246400-23251000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:23246400-23251400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:23246400-23253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:23246400-23259400	Weak transcription	Osteobl	bone
26	chr3:23246400-23261200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
28	chr3:23246600-23248800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr3:23246600-23249200	Enhancers	Brain Hippocampus Middle	brain
30	chr3:23246600-23251200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:23246600-23251200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:23246600-23251200	Weak transcription	HMEC	breast
33	chr3:23246600-23251400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:23246600-23252800	Weak transcription	HUVEC	blood vessel
35	chr3:23246600-23254800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:23246600-23258800	Weak transcription	Fetal Lung	lung
37	chr3:23246600-23259000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:23246600-23259000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:23246600-23259200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:23246600-23259200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:23246600-23260000	Weak transcription	NHEK	skin
42	chr3:23246600-23260800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:23246800-23248800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:23246800-23249000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:23246800-23251200	Weak transcription	Liver	Liver
47	chr3:23246800-23252200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:23246800-23259000	Weak transcription	NHLF	lung
49	chr3:23246800-23259800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:23247000-23250600	Weak transcription	Monocytes-CD14+_RO01746	blood

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