Variant report

Variant	rs73406509
Chromosome Location	chr15:42842061-42842062
allele	A/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	GATA1	chr15:42840433-42842436	PBDE	blood:	n/a	chr15:42841996-42842012 chr15:42841999-42842008 chr15:42842001-42842008 chr15:42842001-42842008 chr15:42841994-42842015 chr15:42842001-42842011 chr15:42842001-42842008
2	MXI1	chr15:42842008-42842291	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr15:42841911-42842229	K562	blood:	n/a	n/a
4	MAX	chr15:42841847-42842523	K562	blood:	n/a	n/a
5	POLR2A	chr15:42841915-42842422	HL-60	blood:	n/a	n/a
6	MAX	chr15:42842016-42842234	Hela-S3	cervix:	n/a	n/a
7	ZNF384	chr15:42841837-42842533	K562	blood:	n/a	n/a
8	CEBPB	chr15:42841989-42842262	Hela-S3	cervix:	n/a	n/a
9	TAL1	chr15:42841945-42842204	K562	blood:	n/a	n/a
10	CEBPB	chr15:42841949-42842253	K562	blood:	n/a	n/a
11	TAF1	chr15:42842049-42842243	K562	blood:	n/a	n/a
12	MAX	chr15:42841984-42842309	NB4	blood:	n/a	n/a
13	MYC	chr15:42842041-42842241	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42786881..42789392-chr15:42840485..42842780,2	K562	blood:
2	chr15:42781742..42786032-chr15:42840388..42842565,4	K562	blood:
3	chr15:42565305..42567163-chr15:42839364..42842481,3	K562	blood:
4	chr15:42841157..42842930-chr15:42866343..42868904,2	MCF-7	breast:
5	chr15:42840090..42842755-chr15:42865653..42870684,5	K562	blood:
6	chr15:42838345..42842657-chr15:42865696..42868936,4	MCF-7	breast:
7	chr15:42837304..42838910-chr15:42839465..42842272,2	MCF-7	breast:
8	chr15:42783961..42786032-chr15:42840679..42842565,2	K562	blood:
9	chr15:41522531..41524126-chr15:42840731..42842443,2	K562	blood:

Variant related genes	Relation type
LRRC57	TF binding region
ENSG00000103994	Chromatin interaction
ENSG00000178997	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000214013	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000103978	Chromatin interaction
ENSG00000159433	Chromatin interaction
ENSG00000187446	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044866	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11541527	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090286	0.85[AFR][1000 genomes]
rs5009460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57249373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57349778	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58122107	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58562675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58952814	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59058205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59091063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60060355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60168929	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60606292	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60697170	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60839827	1.00[AMR][1000 genomes]
rs61368952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61474811	0.85[AMR][1000 genomes]
rs6493048	0.92[AFR][1000 genomes]
rs6493049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493050	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166633	0.87[AMR][1000 genomes]
rs7172064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7172955	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7175059	0.87[AMR][1000 genomes]
rs7178822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7181938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402762	0.85[AMR][1000 genomes]
rs73402776	0.85[AMR][1000 genomes]
rs73402796	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404708	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404729	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404754	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406553	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406557	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs768118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8023948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8027207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033810	1.00[AMR][1000 genomes]
rs8034001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035877	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8036927	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8037277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 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	chr15:42839400-42842200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:42839600-42842600	Active TSS	GM12878-XiMat	blood
3	chr15:42839800-42842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:42839800-42842200	Active TSS	A549	lung
5	chr15:42839800-42842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:42839800-42842800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr15:42840000-42842200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:42840000-42842200	Active TSS	Fetal Muscle Trunk	muscle
9	chr15:42840000-42842400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:42840000-42842400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:42840000-42842400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr15:42840000-42842400	Active TSS	HSMMtube	muscle
13	chr15:42840000-42842600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:42840200-42842200	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr15:42840200-42842200	Active TSS	Psoas Muscle	Psoas
16	chr15:42840200-42842400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:42840200-42842400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr15:42840200-42842400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:42840200-42842400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:42840200-42842600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr15:42840200-42842600	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr15:42840200-42842600	Active TSS	NHLF	lung
23	chr15:42840400-42842200	Active TSS	HSMM	muscle
24	chr15:42840400-42842400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:42840400-42842400	Active TSS	Rectal Smooth Muscle	rectum
26	chr15:42840400-42842400	Active TSS	NH-A	brain
27	chr15:42840600-42842200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:42840600-42842400	Active TSS	Stomach Smooth Muscle	stomach
29	chr15:42841000-42842600	Active TSS	Colonic Mucosa	Colon
30	chr15:42841200-42842200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr15:42841200-42842400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr15:42841200-42842400	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr15:42841600-42842200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:42841600-42842800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:42841600-42850800	Weak transcription	Pancreas	Pancrea
36	chr15:42841600-42851000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:42841600-42851200	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:42841600-42851600	Weak transcription	Lung	lung
39	chr15:42841600-42852000	Weak transcription	Gastric	stomach
40	chr15:42841600-42853600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr15:42841600-42854200	Weak transcription	Aorta	Aorta
42	chr15:42841600-42854200	Weak transcription	Esophagus	oesophagus
43	chr15:42841600-42854200	Weak transcription	Spleen	Spleen
44	chr15:42841600-42866800	Weak transcription	Stomach Mucosa	stomach
45	chr15:42841800-42842200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr15:42841800-42842200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:42841800-42842200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr15:42841800-42842200	Flanking Active TSS	Fetal Stomach	stomach
49	chr15:42841800-42842400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr15:42841800-42842400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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