Variant report

Variant	rs13083195
Chromosome Location	chr3:139067890-139067891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:139065642-139069144	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139066217..139069193-chr3:139069576..139072044,3	MCF-7	breast:
2	chr3:139066912..139069879-chr3:139106229..139109511,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPB2-1	chr3:139067866-139068213	ENSG00000272656.1

Variant related genes	Relation type
MRPS22	TF binding region
ENSG00000184432	Chromatin interaction
ENSG00000175110	Chromatin interaction
ENSG00000252245	Chromatin interaction
ENSG00000248932	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1044826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10460845	0.81[ASN][1000 genomes]
rs10935320	0.95[ASN][1000 genomes]
rs10935323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488939	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12494806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12695698	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12695699	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12695700	0.83[AMR][1000 genomes]
rs13060697	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13074208	0.83[AMR][1000 genomes]
rs13085888	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086868	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs13089007	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089090	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13092507	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13092935	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1586861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1586863	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1586864	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17336869	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1907687	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2233811	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2233815	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2349059	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34623690	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3772877	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772878	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772879	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3821544	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821545	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4383548	0.81[AMR][1000 genomes]
rs4544576	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683818	0.81[AMR][1000 genomes]
rs67929453	0.90[ASN][1000 genomes]
rs6798217	0.81[AMR][1000 genomes]
rs7374385	0.83[EUR][1000 genomes]
rs9289576	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964227	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs973691	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812192	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9818691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9825064	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831108	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834607	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9835241	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs9848241	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9849039	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9849578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9853350	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9860201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9860521	0.83[AMR][1000 genomes]
rs9868544	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9882014	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139063800-139070000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:139064000-139070200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:139064200-139068200	Weak transcription	Stomach Mucosa	stomach
7	chr3:139064200-139068200	Weak transcription	A549	lung
8	chr3:139064200-139072600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
11	chr3:139064600-139069600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:139064800-139068000	Weak transcription	NHDF-Ad	bronchial
13	chr3:139064800-139068600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:139064800-139068800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:139064800-139071200	Weak transcription	Fetal Heart	heart
16	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
17	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
18	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
19	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
20	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:139065000-139103800	Strong transcription	HSMM	muscle
22	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:139065200-139069000	Weak transcription	Small Intestine	intestine
24	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:139065200-139073200	Strong transcription	K562	blood
26	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:139065400-139068400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:139065400-139073800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:139065400-139102600	Strong transcription	Osteobl	bone
41	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
43	chr3:139065600-139068200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:139065600-139070800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:139065600-139070800	Strong transcription	Fetal Stomach	stomach
46	chr3:139065600-139071000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr3:139065600-139073200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:139065600-139077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:139065600-139079600	Strong transcription	Fetal Lung	lung
50	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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