Variant report

Variant	rs41286945
Chromosome Location	chr13:39613579-39613580
allele	A/T
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	CEBPB	chr13:39613407-39613601	A549	lung:	n/a	chr13:39613522-39613535 chr13:39613522-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613522-39613535 chr13:39613524-39613533
2	MAX	chr13:39610127-39614057	NB4	blood:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
3	POLR2A	chr13:39611551-39613699	GM18526	blood:	n/a	n/a
4	E2F4	chr13:39613391-39613636	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr13:39611416-39613914	GM19099	blood:	n/a	n/a
6	MYC	chr13:39610008-39613668	NB4	blood:	n/a	chr13:39610504-39610514 chr13:39610831-39610839
7	CEBPB	chr13:39612835-39613677	IMR90	lung:	n/a	chr13:39613522-39613535 chr13:39613522-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613522-39613535 chr13:39613524-39613533
8	POLR2A	chr13:39611578-39613908	GM18505	blood:	n/a	n/a
9	CEBPB	chr13:39613381-39613612	K562	blood:	n/a	chr13:39613522-39613535 chr13:39613522-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613522-39613535 chr13:39613524-39613533
10	RCOR1	chr13:39613340-39613767	K562	blood:	n/a	n/a
11	FOXA1	chr13:39613188-39613583	HepG2	liver:	n/a	chr13:39613425-39613440
12	EP300	chr13:39613527-39613932	K562	blood:	n/a	n/a
13	CEBPB	chr13:39613337-39613669	HepG2	liver:	n/a	chr13:39613522-39613535 chr13:39613522-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613522-39613535 chr13:39613524-39613533
14	POLR2A	chr13:39611594-39613785	GM12892	blood:	n/a	n/a
15	CEBPB	chr13:39613385-39613688	Hela-S3	cervix:	n/a	chr13:39613522-39613535 chr13:39613522-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613524-39613533 chr13:39613522-39613535 chr13:39613524-39613533
16	TBP	chr13:39613341-39613597	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr13:39610377-39613654	GM12891	blood:	n/a	n/a
18	FOXA1	chr13:39613194-39613694	HepG2	liver:	n/a	chr13:39613425-39613440
19	FOXA1	chr13:39613198-39613712	HepG2	liver:	n/a	chr13:39613425-39613440

No.	Distal block	Cell Line	Cell type
1	chr13:39520213..39521754-chr13:39613104..39615261,2	MCF-7	breast:
2	chr1:149223559..149225520-chr13:39611961..39613912,2	MCF-7	breast:
3	chr13:39584395..39587085-chr13:39611673..39614003,2	MCF-7	breast:
4	chr13:39610419..39613692-chr13:39616080..39618520,4	K562	blood:

Variant related genes	Relation type
PROSER1	TF binding region
NHLRC3	TF binding region
ENSG00000206737	Chromatin interaction
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12428338	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12428487	0.82[AMR][1000 genomes]
rs12429615	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12430798	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12431010	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12431083	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12431327	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1575886	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17226184	0.82[AMR][1000 genomes]
rs17226219	0.82[AMR][1000 genomes]
rs17226809	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17235076	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17235139	1.00[AFR][1000 genomes]
rs17826253	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41286135	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39609000-39615000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:39609000-39615200	Active TSS	K562	blood
3	chr13:39609200-39613600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:39609200-39613800	Active TSS	GM12878-XiMat	blood
5	chr13:39609400-39613800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr13:39609400-39613800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:39609600-39613600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:39609600-39613600	Active TSS	Ovary	ovary
9	chr13:39609600-39613600	Active TSS	Right Atrium	heart
10	chr13:39609600-39613600	Active TSS	Right Ventricle	heart
11	chr13:39609600-39613800	Active TSS	Fetal Muscle Leg	muscle
12	chr13:39609600-39613800	Active TSS	NHEK	skin
13	chr13:39609600-39614000	Active TSS	Hela-S3	cervix
14	chr13:39609600-39614200	Active TSS	Fetal Intestine Large	intestine
15	chr13:39609600-39614800	Active TSS	Placenta	Placenta
16	chr13:39609800-39613600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr13:39609800-39613600	Active TSS	Fetal Thymus	thymus
18	chr13:39609800-39613800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:39609800-39614400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:39610000-39613600	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr13:39610000-39613600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:39610200-39613800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:39610200-39613800	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr13:39610200-39613800	Active TSS	Brain Germinal Matrix	brain
25	chr13:39610200-39613800	Active TSS	Fetal Intestine Small	intestine
26	chr13:39610200-39613800	Active TSS	Fetal Stomach	stomach
27	chr13:39610400-39613600	Active TSS	Fetal Muscle Trunk	muscle
28	chr13:39610600-39613600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr13:39611000-39614000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr13:39611200-39613600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr13:39611200-39613600	Active TSS	Thymus	Thymus
32	chr13:39611400-39613600	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr13:39611400-39613800	Active TSS	Brain Anterior Caudate	brain
34	chr13:39611400-39613800	Active TSS	Brain Hippocampus Middle	brain
35	chr13:39612600-39613600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr13:39612600-39613800	Flanking Active TSS	HUVEC	blood vessel
37	chr13:39612600-39614000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:39612800-39614000	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr13:39612800-39614000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:39612800-39614000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr13:39613000-39613600	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr13:39613000-39613600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr13:39613000-39613600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr13:39613000-39613800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr13:39613000-39613800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr13:39613000-39613800	Active TSS	HMEC	breast
47	chr13:39613000-39614800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr13:39613000-39629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr13:39613000-39636200	Weak transcription	Spleen	Spleen
50	chr13:39613200-39613600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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