Variant report

Variant	rs59958973
Chromosome Location	chr3:139071227-139071228
allele	C/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	chr3:139069653-139075359	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:139070570-139071473	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:139070258-139074075	U87	brain:	n/a	n/a
4	POLR2A	chr3:139069657-139075279	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:139070257-139075369	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:139069579-139081379	K562	blood:	n/a	n/a
7	POLR2A	chr3:139070404-139071334	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr3:139071057-139072329	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:139071170-139071547	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:139070268-139071965	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:139070264-139071988	U87	brain:	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	chr3:139069545..139071790-chr3:139077867..139079665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272656	TF binding region
ENSG00000175110	Chromatin interaction
ENSG00000184432	Chromatin interaction
ENSG00000272656	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10513063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1602626	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1602628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17316181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17335312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17395611	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17494356	0.81[ASN][1000 genomes]
rs17560106	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1844977	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289348	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2289350	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2291555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772876	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs41356949	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs41399544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922868	0.85[ASN][1000 genomes]
rs56993164	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57356584	0.89[EUR][1000 genomes]
rs57995350	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58060926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59628512	0.85[ASN][1000 genomes]
rs59960641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61034702	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61613889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61680644	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][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	chr3:139064000-139073400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:139064000-139073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:139064000-139073600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:139064200-139072600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:139064200-139089200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:139064400-139097200	Strong transcription	Fetal Muscle Leg	muscle
7	chr3:139064800-139074800	Weak transcription	Right Atrium	heart
8	chr3:139064800-139094600	Strong transcription	Primary B cells from cord blood	blood
9	chr3:139065000-139096200	Strong transcription	Fetal Intestine Large	intestine
10	chr3:139065000-139101200	Strong transcription	Primary T cells from cord blood	blood
11	chr3:139065000-139103800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:139065000-139103800	Strong transcription	HSMM	muscle
13	chr3:139065000-139104000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:139065200-139073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:139065200-139073200	Strong transcription	K562	blood
16	chr3:139065200-139089200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:139065200-139093600	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:139065200-139096800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:139065200-139098000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:139065200-139102000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:139065200-139102200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:139065400-139073800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:139065400-139077000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:139065400-139077600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:139065400-139097600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:139065400-139102200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:139065400-139102400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr3:139065400-139102600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:139065400-139102600	Strong transcription	Osteobl	bone
30	chr3:139065400-139103600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:139065400-139103800	Strong transcription	Fetal Thymus	thymus
32	chr3:139065600-139073200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:139065600-139077400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:139065600-139079600	Strong transcription	Fetal Lung	lung
35	chr3:139065600-139100200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:139065600-139101800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:139065600-139102400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:139065600-139102400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:139065600-139102400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:139065600-139103600	Strong transcription	HUVEC	blood vessel
41	chr3:139065600-139103600	Strong transcription	NH-A	brain
42	chr3:139065600-139103800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:139065600-139103800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:139065800-139071800	Strong transcription	Rectal Smooth Muscle	rectum
45	chr3:139065800-139072000	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:139065800-139072400	Strong transcription	HSMMtube	muscle
47	chr3:139065800-139073000	Strong transcription	Brain Substantia Nigra	brain
48	chr3:139065800-139074200	Strong transcription	Adipose Nuclei	Adipose
49	chr3:139065800-139078000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:139065800-139080800	Strong transcription	Brain Germinal Matrix	brain

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