Variant report

Variant	rs9316482
Chromosome Location	chr13:50572688-50572689
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr13:50570246-50572731	H1-neurons	neurons:	n/a	chr13:50570689-50570702
2	CHD1	chr13:50572551-50573326	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr13:50569806-50572944	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr13:50570414-50572858	SK-N-MC	brain:	n/a	n/a
5	RAD21	chr13:50570119-50572813	SK-N-SH	brain:	n/a	chr13:50571462-50571476 chr13:50571466-50571478 chr13:50571461-50571480
6	POLR2A	chr13:50569571-50574166	GM12891	blood:	n/a	n/a
7	POLR2A	chr13:50572290-50572694	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr13:50569853-50572808	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50509071..50511034-chr13:50570092..50572951,3	K562	blood:
2	chr13:50571846..50573402-chr13:50576852..50578789,2	MCF-7	breast:
3	chr13:50568991..50573569-chr13:50697831..50701767,8	K562	blood:
4	chr13:50571599..50573670-chr13:50694075..50695912,2	MCF-7	breast:
5	chr13:50365087..50367801-chr13:50569333..50572997,5	MCF-7	breast:
6	chr13:50571255..50572923-chr13:50651167..50653768,2	MCF-7	breast:
7	chr13:50572525..50574239-chr13:50585255..50587483,2	MCF-7	breast:
8	chr13:50571282..50572929-chr13:50585786..50587490,2	MCF-7	breast:
9	chr13:50572352..50574935-chr13:50588640..50591580,2	K562	blood:
10	chr13:50569748..50573186-chr13:50654848..50657793,4	MCF-7	breast:
11	chr13:50365228..50367548-chr13:50571238..50573275,2	K562	blood:
12	chr13:50569852..50573038-chr13:50651628..50659276,11	K562	blood:
13	chr13:50569462..50575212-chr13:50651363..50657415,15	K562	blood:
14	chr13:50569500..50573569-chr13:50696112..50701767,10	K562	blood:

No data

Variant related genes	Relation type
TRIM13	TF binding region
MIR3613	TF binding region
ENSG00000198553	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000123178	Chromatin interaction
ENSG00000176124	Chromatin interaction
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11839292	0.89[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12876820	0.87[ASN][1000 genomes]
rs1323450	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2066544	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066581	0.96[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2066593	0.92[CEU][hapmap]
rs2407884	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760911	0.92[CEU][hapmap];0.91[YRI][hapmap]
rs6561570	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7318151	0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9316484	0.87[ASN][1000 genomes]
rs9526629	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535403	0.87[ASN][1000 genomes]
rs9535410	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535411	1.00[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535414	0.92[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535415	0.87[ASN][1000 genomes]
rs9535416	0.92[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9740075	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50569800-50573600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:50570000-50572800	Active TSS	Aorta	Aorta
3	chr13:50570000-50572800	Active TSS	Right Atrium	heart
4	chr13:50570000-50574000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr13:50570200-50572800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:50570200-50572800	Active TSS	Left Ventricle	heart
7	chr13:50570200-50573200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:50570200-50573200	Active TSS	A549	lung
9	chr13:50570200-50573600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:50570400-50573000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:50570400-50573000	Active TSS	NHLF	lung
12	chr13:50571600-50572800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr13:50571600-50573000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr13:50571600-50573000	Active TSS	Brain Germinal Matrix	brain
15	chr13:50571600-50573000	Weak transcription	Spleen	Spleen
16	chr13:50571800-50572800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:50571800-50572800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:50571800-50572800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
19	chr13:50571800-50572800	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr13:50571800-50572800	Weak transcription	Pancreas	Pancrea
21	chr13:50571800-50573000	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr13:50571800-50585200	Weak transcription	Gastric	stomach
23	chr13:50572000-50572800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr13:50572000-50572800	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
25	chr13:50572000-50572800	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr13:50572000-50572800	Flanking Active TSS	Fetal Brain Male	brain
27	chr13:50572000-50572800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr13:50572000-50572800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
29	chr13:50572000-50572800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:50572000-50573000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr13:50572000-50573000	Flanking Active TSS	Osteobl	bone
32	chr13:50572000-50573400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr13:50572000-50573400	Enhancers	Small Intestine	intestine
34	chr13:50572000-50574600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:50572000-50574600	Enhancers	Stomach Mucosa	stomach
36	chr13:50572000-50574800	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr13:50572000-50578400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr13:50572000-50578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr13:50572000-50585800	Weak transcription	Ovary	ovary
40	chr13:50572200-50572800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:50572200-50572800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:50572200-50572800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:50572200-50572800	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr13:50572200-50572800	Flanking Active TSS	Fetal Brain Female	brain
45	chr13:50572200-50572800	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
46	chr13:50572200-50572800	Flanking Active TSS	Hela-S3	cervix
47	chr13:50572200-50572800	Flanking Active TSS	HMEC	breast
48	chr13:50572200-50572800	Transcr. at gene 5' and 3'	NHEK	skin
49	chr13:50572200-50573000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:50572200-50573000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle

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