Variant report

Variant	rs5743838
Chromosome Location	chr3:52260598-52260599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:52260500-52260650	GM12866	blood:	n/a	n/a
2	POLR2A	chr3:52259381-52260798	HL-60	blood:	n/a	n/a
3	CTCF	chr3:52260500-52260650	HepG2	liver:	n/a	n/a
4	CTCF	chr3:52260460-52260610	K562	blood:	n/a	n/a
5	CTCF	chr3:52260406-52260604	GM12891	blood:	n/a	n/a
6	MYC	chr3:52259517-52260700	NB4	blood:	n/a	n/a
7	CTCF	chr3:52260457-52260608	GM12892	blood:	n/a	n/a
8	CTCF	chr3:52260472-52260617	K562	blood:	n/a	n/a
9	CTCF	chr3:52260500-52260650	GM12872	blood:	n/a	n/a
10	ELF1	chr3:52259360-52260612	GM12878	blood:	n/a	chr3:52259659-52259670
11	CTCF	chr3:52260444-52260620	HepG2	liver:	n/a	n/a
12	CUX1	chr3:52260557-52260603	GM12878	blood:	n/a	n/a
13	CTCF	chr3:52260480-52260630	GM12869	blood:	n/a	n/a
14	POLR2A	chr3:52259383-52260773	Raji	blood:	n/a	n/a
15	POLR2A	chr3:52259432-52260798	GM18505	blood:	n/a	n/a
16	CTCF	chr3:52260461-52260599	GM19240	blood:	n/a	n/a
17	CTCF	chr3:52260500-52260650	GM12873	blood:	n/a	n/a
18	CTCF	chr3:52260472-52260603	GM12878	blood:	n/a	n/a
19	PML	chr3:52260542-52260993	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:52259415-52261103	GM12891	blood:	n/a	n/a
21	CTCF	chr3:52260500-52260650	GM12865	blood:	n/a	n/a
22	CTCF	chr3:52260520-52260670	GM12868	blood:	n/a	n/a
23	POLR2A	chr3:52259368-52260624	GM19193	blood:	n/a	n/a
24	POLR2A	chr3:52259380-52261016	HL-60	blood:	n/a	n/a
25	CTCF	chr3:52260491-52260604	Hela-S3	cervix:	n/a	n/a
26	MTA3	chr3:52259270-52260934	GM12878	blood:	n/a	n/a
27	CTCF	chr3:52260460-52260610	GM12871	blood:	n/a	n/a
28	RUNX3	chr3:52260467-52260776	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:52259400-52260673	GM19099	blood:	n/a	n/a
30	RUNX3	chr3:52260571-52260872	GM12878	blood:	n/a	n/a
31	MAX	chr3:52259419-52260618	NB4	blood:	n/a	n/a
32	CTCF	chr3:52260520-52260670	GM12873	blood:	n/a	n/a
33	EBF1	chr3:52260356-52260695	GM12878	blood:	n/a	n/a
34	CTCF	chr3:52260460-52260610	GM12869	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52259472..52263342-chr3:52269626..52274061,4	MCF-7	breast:

No data

Variant related genes	Relation type
TLR9	TF binding region
ENSG00000243224	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17052020	1.00[EUR][1000 genomes]
rs17052095	1.00[AMR][1000 genomes]
rs56990501	1.00[EUR][1000 genomes]
rs61738524	1.00[AMR][1000 genomes]
rs6445259	1.00[EUR][1000 genomes]
rs6784563	1.00[EUR][1000 genomes]
rs6784653	1.00[EUR][1000 genomes]
rs6797786	1.00[EUR][1000 genomes]
rs7614535	1.00[EUR][1000 genomes]
rs7615736	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7617023	1.00[EUR][1000 genomes]
rs7623076	1.00[EUR][1000 genomes]
rs7625515	1.00[EUR][1000 genomes]
rs7636412	1.00[EUR][1000 genomes]
rs7652984	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	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
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247200-52263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52249600-52263400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52249800-52262400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52249800-52262400	Weak transcription	Aorta	Aorta
6	chr3:52250000-52261400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:52250000-52261800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:52250000-52262200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:52250000-52262600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:52250200-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:52251000-52261800	Weak transcription	Fetal Brain Female	brain
12	chr3:52251000-52266600	Weak transcription	Fetal Brain Male	brain
13	chr3:52251200-52262200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:52251400-52262000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:52251400-52263200	Weak transcription	A549	lung
16	chr3:52251600-52261600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:52251600-52261800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:52251600-52262400	Weak transcription	NHLF	lung
19	chr3:52251600-52262400	Weak transcription	Osteobl	bone
20	chr3:52251600-52262800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:52251600-52262800	Weak transcription	NHDF-Ad	bronchial
22	chr3:52251600-52263600	Weak transcription	HSMM	muscle
23	chr3:52251600-52264200	Weak transcription	HSMMtube	muscle
24	chr3:52251600-52266600	Weak transcription	Psoas Muscle	Psoas
25	chr3:52252200-52261400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:52252200-52261800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:52253000-52262000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:52253000-52262800	Weak transcription	Small Intestine	intestine
29	chr3:52253200-52261800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:52253200-52263000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
32	chr3:52253400-52262400	Weak transcription	NH-A	brain
33	chr3:52253400-52263400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:52253400-52264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:52253800-52263200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52254000-52263000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52254800-52261400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:52255000-52261400	Weak transcription	Liver	Liver
39	chr3:52255000-52261600	Weak transcription	Brain Anterior Caudate	brain
40	chr3:52255000-52261600	Weak transcription	NHEK	skin
41	chr3:52255000-52261800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:52255000-52262000	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:52255000-52262000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:52255000-52262400	Weak transcription	Pancreas	Pancrea
45	chr3:52255000-52262600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:52255000-52262800	Weak transcription	Brain Angular Gyrus	brain
47	chr3:52255000-52263000	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:52255000-52263200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:52255000-52263800	Weak transcription	HUVEC	blood vessel
50	chr3:52255000-52263800	Weak transcription	K562	blood

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