Variant report

Variant	rs1980143
Chromosome Location	chr3:150948356-150948357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10212582	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1048408	0.89[CEU][hapmap]
rs10513392	0.90[CEU][hapmap]
rs11711104	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11719936	0.90[CEU][hapmap]
rs13317873	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472122	0.89[CEU][hapmap]
rs1565574	0.89[CEU][hapmap]
rs1882014	0.89[CEU][hapmap]
rs1882015	0.90[CEU][hapmap]
rs1882016	0.89[CEU][hapmap]
rs1920395	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2904430	0.90[CEU][hapmap]
rs3846072	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679772	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680254	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680257	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680260	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680273	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440730	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782715	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6807308	0.96[CEU][hapmap]
rs6809692	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73021201	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617677	0.96[CEU][hapmap]
rs7653603	0.96[CEU][hapmap]
rs8180086	0.89[CEU][hapmap]
rs9810067	0.90[CEU][hapmap]
rs9815520	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9827619	0.90[CEU][hapmap]
rs9828553	0.89[CEU][hapmap]
rs9835328	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9853297	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9870740	0.96[CEU][hapmap]
rs9875152	0.90[CEU][hapmap]
rs9880339	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150928800-150952800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:150928800-150953000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:150938600-150948600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:150942200-150948600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:150943200-150948600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:150944000-150948600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:150946200-150979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:150946400-150948400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:150946400-150948600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:150946600-150948600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:150946600-150950800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:150946600-150957800	Weak transcription	Gastric	stomach
13	chr3:150946800-150948400	Weak transcription	Adipose Nuclei	Adipose
14	chr3:150946800-150948600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:150946800-150948600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:150946800-150948600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:150946800-150948800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:150946800-150951800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:150946800-150956600	Weak transcription	Fetal Lung	lung
20	chr3:150946800-150969200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:150946800-150983600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:150947000-150948400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:150947200-150948600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:150947800-150948600	Enhancers	Placenta	Placenta
25	chr3:150948000-150948400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr3:150948000-150948400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:150948000-150948400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:150948000-150948400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:150948000-150948600	Enhancers	GM12878-XiMat	blood
30	chr3:150948000-150948800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr3:150948000-150948800	Enhancers	Fetal Thymus	thymus
32	chr3:150948000-150949000	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr3:150948000-150949000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:150948000-150949000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:150948000-150949000	Enhancers	Dnd41	blood
36	chr3:150948000-150949200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr3:150948000-150949200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:150948000-150949200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr3:150948000-150949200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:150948000-150949200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:150948000-150949200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:150948200-150948400	Enhancers	Primary T cells from cord blood	blood
43	chr3:150948200-150948400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:150948200-150948400	Enhancers	Brain Substantia Nigra	brain
45	chr3:150948200-150948400	Enhancers	NHEK	skin
46	chr3:150948200-150948400	Enhancers	NHLF	lung
47	chr3:150948200-150948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:150948200-150948800	Enhancers	Brain Anterior Caudate	brain
49	chr3:150948200-150949000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:150948200-150949000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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