Variant report

Variant	rs900949
Chromosome Location	chr3:136751674-136751675
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136751186..136751967-chr3:136828909..136829867,2	MCF-7	breast:
2	chr3:136750966..136751930-chr3:137690153..137690670,2	K562	blood:
3	chr3:136751027..136751908-chr3:136823889..136824681,2	MCF-7	breast:
4	chr3:136750951..136751906-chr3:137664906..137665965,5	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs108858	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs13095028	0.81[CEU][hapmap]
rs13095034	0.88[EUR][1000 genomes]
rs1385306	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1470142	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1654900	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654901	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682361	0.88[EUR][1000 genomes]
rs1682362	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682363	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682364	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682365	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1682366	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs181732	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2086880	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2117008	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2344092	0.84[EUR][1000 genomes]
rs34564994	0.86[EUR][1000 genomes]
rs361227	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361228	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361229	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361231	0.86[EUR][1000 genomes]
rs361232	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs361233	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs361234	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs361235	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4678278	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4678281	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55781515	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6439677	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439678	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6763000	0.82[AMR][1000 genomes]
rs6766766	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766858	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802479	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754694	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640951	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7646307	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835627	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs835628	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835629	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835630	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835631	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs835651	0.84[EUR][1000 genomes]
rs835652	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs900947	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs900948	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900950	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9681468	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9817061	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9827066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845076	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs9850024	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9854795	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9874615	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs999038	0.81[AMR][1000 genomes];0.91[EUR][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	nsv877534	chr3:136676303-136765859	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv524856	chr3:136693459-137190765	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012111	chr3:136695367-137343430	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136742800-136751800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:136745800-136755000	Weak transcription	NHEK	skin
3	chr3:136748000-136754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:136750800-136752000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:136751000-136751800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:136751000-136751800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:136751000-136751800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:136751000-136752000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:136751000-136752000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:136751000-136752000	Active TSS	Stomach Smooth Muscle	stomach
11	chr3:136751000-136752000	Active TSS	A549	lung
12	chr3:136751000-136752400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:136751200-136751800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:136751200-136751800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr3:136751200-136751800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr3:136751200-136751800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
17	chr3:136751200-136751800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
18	chr3:136751200-136751800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
19	chr3:136751200-136751800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:136751200-136751800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr3:136751200-136751800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:136751200-136751800	Active TSS	Brain Anterior Caudate	brain
23	chr3:136751200-136751800	Active TSS	Brain Germinal Matrix	brain
24	chr3:136751200-136751800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:136751200-136751800	Active TSS	Brain Substantia Nigra	brain
26	chr3:136751200-136751800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr3:136751200-136751800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
28	chr3:136751200-136751800	Active TSS	Fetal Brain Female	brain
29	chr3:136751200-136751800	Active TSS	Psoas Muscle	Psoas
30	chr3:136751200-136751800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr3:136751200-136751800	Active TSS	NHDF-Ad	bronchial
32	chr3:136751200-136751800	Active TSS	NHLF	lung
33	chr3:136751200-136752000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:136751200-136752000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:136751200-136752000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:136751200-136752000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:136751200-136752000	Flanking Active TSS	Liver	Liver
38	chr3:136751200-136752000	Active TSS	Brain Angular Gyrus	brain
39	chr3:136751200-136752000	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr3:136751200-136752000	Flanking Bivalent TSS/Enh	HepG2	liver
41	chr3:136751200-136752000	Active TSS	HSMM	muscle
42	chr3:136751200-136752000	Active TSS	Osteobl	bone
43	chr3:136751400-136751800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:136751400-136751800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:136751400-136751800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr3:136751400-136751800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr3:136751400-136751800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:136751400-136751800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
49	chr3:136751400-136751800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:136751400-136751800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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