Variant report

Variant	rs13316522
Chromosome Location	chr3:158389653-158389654
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	chr3:158389464-158390742	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:158389532-158390889	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:158389479-158390945	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:158389545-158390856	A549	lung:	n/a	n/a
5	POLR2A	chr3:158389546-158389717	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:158388424-158390772	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr3:158389578-158390852	MCF-7	breast:	n/a	n/a
8	MYC	chr3:158389617-158389816	MCF10A-Er-Src	breast:	n/a	n/a
9	CHD1	chr3:158389424-158389773	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr3:158389652-158391089	MCF-7	breast:	n/a	n/a
11	KAP1	chr3:158389580-158390932	HEK293	kidney:	n/a	n/a
12	MAZ	chr3:158389398-158390863	IMR90	lung:	n/a	chr3:158389586-158389597
13	POLR2A	chr3:158389496-158390782	GM18505	blood:	n/a	n/a
14	WRNIP1	chr3:158389652-158390329	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:158389396-158390808	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr3:158389641-158389907	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:158381091-158391011	PBDE	blood:	n/a	n/a
18	CTCF	chr3:158389528-158391125	A549	lung:	n/a	chr3:158390572-158390580 chr3:158390569-158390587 chr3:158390571-158390592
19	MXI1	chr3:158389379-158391135	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158387511..158389723-chr3:158444279..158445857,2	MCF-7	breast:
2	chr3:158388083..158390320-chr3:158417482..158420125,2	MCF-7	breast:
3	chr3:158378888..158380588-chr3:158388656..158390307,2	MCF-7	breast:
4	chr3:158362274..158363819-chr3:158388698..158391198,2	MCF-7	breast:

Variant related genes	Relation type
LXN	TF binding region
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs28825222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28838673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28892926	1.00[AFR][1000 genomes]
rs60378784	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6781894	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73024716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73028908	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73028942	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73028945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73030846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810232	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9814215	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9815159	1.00[AMR][1000 genomes]
rs9828477	1.00[AMR][1000 genomes]
rs9830695	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833662	1.00[AMR][1000 genomes]
rs9846674	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9860148	1.00[AMR][1000 genomes]
rs9864685	1.00[AMR][1000 genomes]
rs9867378	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 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	chr3:158362800-158389800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:158362800-158390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:158364800-158391000	Strong transcription	Dnd41	blood
4	chr3:158372200-158389800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:158376600-158390200	Strong transcription	HSMM	muscle
6	chr3:158379400-158389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:158379400-158389800	Weak transcription	Right Ventricle	heart
8	chr3:158379400-158389800	Weak transcription	Spleen	Spleen
9	chr3:158379600-158389800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:158381600-158389800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:158382800-158389800	Weak transcription	Esophagus	oesophagus
12	chr3:158384800-158389800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:158385600-158389800	Weak transcription	Psoas Muscle	Psoas
14	chr3:158385600-158390000	Weak transcription	Aorta	Aorta
15	chr3:158386200-158407800	Weak transcription	HepG2	liver
16	chr3:158386600-158389800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:158386600-158389800	Weak transcription	Small Intestine	intestine
18	chr3:158386600-158390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:158386800-158389800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:158386800-158389800	Weak transcription	Left Ventricle	heart
21	chr3:158387600-158389800	Weak transcription	NHDF-Ad	bronchial
22	chr3:158388000-158389800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:158388000-158389800	Weak transcription	Liver	Liver
24	chr3:158388200-158389800	Weak transcription	Placenta	Placenta
25	chr3:158388600-158390600	Active TSS	Fetal Lung	lung
26	chr3:158388800-158389800	Flanking Active TSS	HUVEC	blood vessel
27	chr3:158388800-158390200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:158388800-158390600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:158388800-158390800	Active TSS	Fetal Intestine Large	intestine
30	chr3:158389000-158389800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:158389000-158389800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:158389000-158389800	Flanking Active TSS	GM12878-XiMat	blood
33	chr3:158389000-158390000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:158389000-158390200	Strong transcription	HSMMtube	muscle
35	chr3:158389000-158390600	Active TSS	NHLF	lung
36	chr3:158389000-158390600	Active TSS	Osteobl	bone
37	chr3:158389000-158390800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:158389200-158389800	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr3:158389200-158390000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr3:158389200-158390000	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr3:158389200-158390000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:158389200-158390000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr3:158389200-158390200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr3:158389200-158390200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr3:158389200-158390600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:158389200-158390600	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr3:158389200-158390600	Active TSS	A549	lung
48	chr3:158389200-158391200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:158389400-158389800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr3:158389400-158389800	Enhancers	Primary monocytes fromperipheralblood	blood

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