Variant report

Variant	rs11712500
Chromosome Location	chr3:23253657-23253658
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23252644..23254931-chr3:23257139..23259977,2	MCF-7	breast:
2	chr3:23243375..23248925-chr3:23249833..23255104,8	MCF-7	breast:
3	chr3:23245201..23247930-chr3:23252122..23255042,2	K562	blood:

Variant related genes	Relation type
ENSG00000233153	Chromatin interaction
ENSG00000182247	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11707094	0.83[ASN][1000 genomes]
rs11707450	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708040	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712582	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11713392	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715035	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17342980	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17401836	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17402378	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1874234	0.84[ASN][1000 genomes]
rs1874503	0.83[ASN][1000 genomes]
rs1994953	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2055156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2055157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2101811	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132144	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2132146	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132148	0.97[ASN][1000 genomes]
rs2201484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2359754	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35194124	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35613382	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4334589	0.92[AFR][1000 genomes]
rs4858063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858487	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858489	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858490	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858495	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858499	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5023615	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59185768	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62252657	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255292	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255293	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6762546	0.80[AMR][1000 genomes]
rs6774214	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6790327	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7621680	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653868	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs903520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs923996	0.97[ASN][1000 genomes]
rs9815299	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9823684	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9836135	0.89[ASN][1000 genomes]
rs9840808	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9841336	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9848389	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849679	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9863465	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9875910	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:23246000-23260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:23246200-23257200	Weak transcription	Ovary	ovary
4	chr3:23246200-23257400	Weak transcription	Left Ventricle	heart
5	chr3:23246200-23258800	Weak transcription	HSMM	muscle
6	chr3:23246200-23259000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:23246200-23259000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:23246200-23259200	Weak transcription	NH-A	brain
9	chr3:23246200-23260600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:23246400-23259400	Weak transcription	Osteobl	bone
12	chr3:23246400-23261200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
14	chr3:23246600-23254800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:23246600-23258800	Weak transcription	Fetal Lung	lung
16	chr3:23246600-23259000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:23246600-23259000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:23246600-23259200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:23246600-23259200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:23246600-23260000	Weak transcription	NHEK	skin
21	chr3:23246600-23260800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:23246800-23259000	Weak transcription	NHLF	lung
24	chr3:23246800-23259800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:23247400-23258400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:23248200-23258400	Weak transcription	Brain Anterior Caudate	brain
27	chr3:23248200-23259000	Weak transcription	A549	lung
28	chr3:23248200-23260600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:23248800-23257200	Weak transcription	Brain Angular Gyrus	brain
30	chr3:23248800-23257400	Weak transcription	Brain Substantia Nigra	brain
31	chr3:23248800-23265800	Weak transcription	Primary T cells from cord blood	blood
32	chr3:23249000-23273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:23249200-23257000	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:23249400-23260600	Weak transcription	HSMMtube	muscle
35	chr3:23250200-23255200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:23250400-23254800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:23250400-23256200	Weak transcription	Fetal Thymus	thymus
38	chr3:23250400-23257400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:23251000-23254600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:23251400-23258200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:23251600-23259200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:23251600-23260400	Weak transcription	HMEC	breast
43	chr3:23251600-23262800	Weak transcription	Adipose Nuclei	Adipose
44	chr3:23251800-23257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:23251800-23260600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:23251800-23260600	Weak transcription	Esophagus	oesophagus
47	chr3:23251800-23260800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:23252400-23258800	Weak transcription	GM12878-XiMat	blood
49	chr3:23252600-23258800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:23252800-23260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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