Variant report

Variant	rs13318570
Chromosome Location	chr3:52313436-52313437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:52311125-52315006	SK-N-SH	brain:	n/a	chr3:52313881-52313895 chr3:52312475-52312484 chr3:52311546-52311555 chr3:52313068-52313082 chr3:52313069-52313083
2	UBTF	chr3:52311612-52313457	K562	blood:	n/a	n/a
3	POLR2A	chr3:52313399-52313734	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr3:52311452-52313631	K562	blood:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
5	POLR2A	chr3:52313306-52314466	SK-N-SH	brain:	n/a	n/a
6	POU2F2	chr3:52312726-52313495	GM12891	blood:	n/a	n/a
7	CHD1	chr3:52310531-52313715	IMR90	lung:	n/a	n/a
8	MXI1	chr3:52310948-52314914	SK-N-SH	brain:	n/a	n/a
9	YY1	chr3:52313380-52313533	K562	blood:	n/a	n/a
10	POLR2A	chr3:52311473-52313658	GM12892	blood:	n/a	n/a
11	PML	chr3:52311346-52313509	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:52311416-52313502	HUVEC	blood vessel:	n/a	n/a
13	ELF1	chr3:52311504-52313530	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:52311101-52313535	GM12878	blood:	n/a	n/a
15	MAX	chr3:52311346-52313584	A549	lung:	n/a	chr3:52311696-52311703 chr3:52312935-52312945
16	POLR2A	chr3:52311448-52313573	HepG2	liver:	n/a	n/a
17	MAZ	chr3:52313418-52313466	GM12878	blood:	n/a	n/a
18	YY1	chr3:52313252-52313609	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:52311387-52313566	K562	blood:	n/a	n/a
20	POLR2A	chr3:52311111-52313571	H1-hESC	embryonic stem cell:	n/a	n/a
21	SMARCB1	chr3:52311645-52313482	Hela-S3	cervix:	n/a	chr3:52312986-52312995
22	POLR2A	chr3:52311366-52313646	GM12892	blood:	n/a	n/a
23	POLR2A	chr3:52311999-52313539	K562	blood:	n/a	n/a
24	E2F6	chr3:52313360-52313577	K562	blood:	n/a	n/a
25	POLR2A	chr3:52311136-52313596	GM12878	blood:	n/a	n/a
26	YY1	chr3:52313188-52313563	K562	blood:	n/a	n/a
27	CTCF	chr3:52313340-52313490	HBMEC	blood vessel:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:28973386..28976212-chr3:52311138..52314136,3	K562	blood:
2	chr3:52269533..52276077-chr3:52310385..52313504,11	MCF-7	breast:
3	chr1:28834867..28836963-chr3:52311963..52313620,2	K562	blood:
4	chr3:52311359..52313564-chr3:52443173..52445594,2	MCF-7	breast:
5	chr3:52312898..52314508-chr3:52316023..52317538,2	MCF-7	breast:
6	chr3:52311763..52314254-chr3:52566006..52568592,3	K562	blood:
7	chr3:52278055..52281861-chr3:52310588..52314481,6	K562	blood:
8	chr3:52312964..52314575-chr3:52349556..52352232,2	K562	blood:
9	chr3:52312779..52315046-chr3:52326364..52328417,2	MCF-7	breast:
10	chr3:52015955..52017820-chr3:52311212..52313632,2	K562	blood:
11	chr3:52297780..52305259-chr3:52310132..52314407,14	MCF-7	breast:
12	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
13	chr3:52269470..52276026-chr3:52310334..52314212,10	MCF-7	breast:
14	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:
15	chr3:52312419..52314160-chr3:52485786..52488594,2	MCF-7	breast:
16	chr3:52311051..52315983-chr3:52317623..52323290,10	MCF-7	breast:
17	chr3:52263787..52265921-chr3:52311180..52314270,4	MCF-7	breast:
18	chr3:52278055..52281861-chr3:52310505..52315451,9	K562	blood:
19	chr3:52270811..52274971-chr3:52310538..52315239,11	K562	blood:
20	chr14:23769376..23771868-chr3:52311164..52313739,2	MCF-7	breast:
21	chr3:52187270..52191492-chr3:52311211..52313437,5	MCF-7	breast:
22	chr3:52312722..52314589-chr3:52419579..52422419,2	MCF-7	breast:
23	chr3:52270811..52276588-chr3:52310648..52314131,11	K562	blood:
24	chr3:52278312..52281288-chr3:52312020..52314246,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYCTK-1	chr3:52312868-52315151	NONHSAT089909

No data

Variant related genes	Relation type
WDR82	TF binding region
ENSG00000235194	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000199150	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000173366	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000164088	Chromatin interaction
ENSG00000207926	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000200087	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17052143	1.00[AMR][1000 genomes]
rs28413740	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28434358	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34540591	1.00[AMR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes]
rs9813468	1.00[AMR][1000 genomes]
rs9813653	1.00[AMR][1000 genomes]
rs9815559	1.00[AMR][1000 genomes]
rs9821916	1.00[AMR][1000 genomes]
rs9824342	1.00[AMR][1000 genomes]
rs9828432	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9828488	1.00[AMR][1000 genomes]
rs9831689	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834363	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9836166	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9843055	1.00[AMR][1000 genomes]
rs9844178	1.00[AMR][1000 genomes]
rs9845752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9868332	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 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	chr3:52309200-52313600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:52310000-52313600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:52310200-52313600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr3:52310200-52313600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:52310200-52313600	Active TSS	K562	blood
6	chr3:52310200-52314000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:52310800-52313600	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr3:52310800-52313800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:52310800-52314400	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:52311000-52313600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:52311000-52313600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:52311000-52313600	Active TSS	Aorta	Aorta
13	chr3:52311000-52314000	Active TSS	NHLF	lung
14	chr3:52311000-52314400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:52311400-52314000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr3:52311400-52314000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:52311600-52314000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr3:52312800-52313600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr3:52312800-52313600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr3:52312800-52313600	Flanking Active TSS	Placenta	Placenta
21	chr3:52312800-52313600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr3:52312800-52314200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr3:52312800-52314400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:52313000-52313600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:52313000-52313600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr3:52313000-52313600	Flanking Active TSS	Fetal Intestine Small	intestine
27	chr3:52313000-52313600	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr3:52313000-52313600	Flanking Active TSS	Thymus	Thymus
29	chr3:52313000-52313600	Flanking Active TSS	HepG2	liver
30	chr3:52313000-52313800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr3:52313000-52313800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr3:52313000-52313800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr3:52313000-52313800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:52313000-52313800	Flanking Active TSS	Fetal Thymus	thymus
35	chr3:52313000-52314000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr3:52313000-52314000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:52313000-52314000	Flanking Active TSS	Dnd41	blood
38	chr3:52313000-52314400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr3:52313200-52313600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:52313200-52313600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:52313200-52313600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52313200-52313600	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr3:52313200-52313600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr3:52313200-52313600	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr3:52313200-52313600	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr3:52313200-52313600	Flanking Active TSS	Fetal Stomach	stomach
47	chr3:52313200-52313600	Flanking Active TSS	Psoas Muscle	Psoas
48	chr3:52313200-52313600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr3:52313200-52313600	Flanking Active TSS	Hela-S3	cervix
50	chr3:52313200-52313600	Flanking Active TSS	NHEK	skin

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