Variant report

Variant	rs73406553
Chromosome Location	chr15:42867673-42867674
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	POLR2A	chr15:42867167-42868154	ProgFib	skin:	n/a	n/a
2	E2F6	chr15:42867132-42868315	A549	lung:	n/a	chr15:42867462-42867473 chr15:42867463-42867475 chr15:42867769-42867779 chr15:42867697-42867706 chr15:42867714-42867726 chr15:42867302-42867312 chr15:42867584-42867596 chr15:42867817-42867826
3	BRCA1	chr15:42867171-42867861	Hela-S3	cervix:	n/a	n/a
4	NFIC	chr15:42867330-42868546	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr15:42867378-42867993	MCF-7	breast:	n/a	n/a
6	JUND	chr15:42867096-42867944	K562	blood:	n/a	chr15:42867696-42867705 chr15:42867816-42867825
7	POLR2A	chr15:42867102-42868182	GM12892	blood:	n/a	n/a
8	NFYA	chr15:42867291-42867884	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr15:42867129-42867887	Hela-S3	cervix:	n/a	chr15:42867209-42867222
10	POLR2A	chr15:42867332-42868307	IMR90	lung:	n/a	n/a
11	MAX	chr15:42866909-42868453	ECC-1	luminal epithelium:	n/a	chr15:42867809-42867818
12	MAX	chr15:42867141-42868356	K562	blood:	n/a	chr15:42867809-42867818
13	POLR2A	chr15:42867443-42867935	GM12878	blood:	n/a	n/a
14	TCF7L2	chr15:42867348-42868229	HCT-116	colon:	n/a	n/a
15	EP300	chr15:42867187-42867720	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:42867214-42867783	K562	blood:	n/a	n/a
17	IRF1	chr15:42867270-42867976	K562	blood:	n/a	chr15:42867696-42867710 chr15:42867753-42867767 chr15:42867440-42867454
18	MAX	chr15:42867025-42868423	SK-N-SH	brain:	n/a	chr15:42867809-42867818
19	ZKSCAN1	chr15:42867384-42867754	Hela-S3	cervix:	n/a	n/a
20	PAX5	chr15:42867204-42867848	GM12878	blood:	n/a	chr15:42867434-42867453
21	MAX	chr15:42867113-42868030	MCF-7	breast:	n/a	chr15:42867809-42867818
22	TAF1	chr15:42867266-42868309	HepG2	liver:	n/a	n/a
23	MAX	chr15:42867055-42868579	HepG2	liver:	n/a	chr15:42867809-42867818
24	BHLHE40	chr15:42867126-42868327	K562	blood:	n/a	chr15:42867776-42867792 chr15:42867765-42867781
25	MYC	chr15:42867122-42868128	A549	lung:	n/a	chr15:42867809-42867818
26	RCOR1	chr15:42867351-42868075	GM12878	blood:	n/a	n/a
27	E2F6	chr15:42866979-42868526	A549	lung:	n/a	chr15:42867462-42867473 chr15:42867463-42867475 chr15:42867769-42867779 chr15:42867697-42867706 chr15:42867714-42867726 chr15:42867302-42867312 chr15:42867584-42867596 chr15:42867817-42867826
28	CCNT2	chr15:42867230-42868278	K562	blood:	n/a	chr15:42868077-42868086
29	TAF1	chr15:42867300-42867996	Hela-S3	cervix:	n/a	n/a
30	MAX	chr15:42867041-42868436	ECC-1	luminal epithelium:	n/a	chr15:42867809-42867818
31	SP1	chr15:42867162-42868005	HepG2	liver:	n/a	chr15:42867561-42867572 chr15:42867528-42867537 chr15:42867437-42867451 chr15:42867818-42867827 chr15:42867698-42867707 chr15:42867823-42867832 chr15:42867696-42867708 chr15:42867816-42867828 chr15:42867442-42867451 chr15:42867657-42867666 chr15:42867440-42867452 chr15:42867816-42867828 chr15:42867697-42867706 chr15:42867693-42867707 chr15:42867696-42867708
32	HEY1	chr15:42867132-42868054	HepG2	liver:	n/a	chr15:42867761-42867776 chr15:42867779-42867794
33	MXI1	chr15:42866252-42869441	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr15:42867295-42868039	GM12891	blood:	n/a	n/a
35	NR2F2	chr15:42867630-42868323	K562	blood:	n/a	n/a
36	POLR2A	chr15:42867238-42868079	K562	blood:	n/a	n/a
37	ELK1	chr15:42867455-42867904	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr15:42867168-42868024	HepG2	liver:	n/a	n/a
39	POLR2A	chr15:42867108-42868165	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr15:42867002-42868493	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr15:42867257-42868002	A549	lung:	n/a	n/a
42	TAF1	chr15:42867259-42868048	SK-N-SH	brain:	n/a	n/a
43	MAX	chr15:42867058-42868069	SK-N-SH	brain:	n/a	chr15:42867809-42867818
44	MAFK	chr15:42867277-42867780	Hela-S3	cervix:	n/a	n/a
45	FOXA1	chr15:42867442-42867756	T-47D	breast:	n/a	n/a
46	MAX	chr15:42867065-42868623	H1-hESC	embryonic stem cell:	n/a	chr15:42867809-42867818
47	EP300	chr15:42867307-42867742	GM12878	blood:	n/a	n/a
48	TEAD4	chr15:42867225-42867805	ECC-1	luminal epithelium:	n/a	n/a
49	TAF1	chr15:42867564-42867957	K562	blood:	n/a	n/a
50	TBP	chr15:42867174-42868543	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42866660..42868750-chr15:42872207..42873779,2	K562	blood:
2	chr15:42838345..42842657-chr15:42865696..42868936,4	MCF-7	breast:
3	chr15:42840104..42842482-chr15:42865653..42867827,2	K562	blood:
4	chr15:42866281..42869584-chr15:42871180..42873707,4	K562	blood:
5	chr15:42838709..42841070-chr15:42866779..42868984,2	MCF-7	breast:
6	chr15:42840090..42842755-chr15:42865653..42870684,5	K562	blood:
7	chr15:42854171..42864590-chr15:42864872..42869799,12	K562	blood:
8	chr15:42801179..42804150-chr15:42867351..42869271,2	K562	blood:
9	chr15:42785710..42787693-chr15:42866156..42868186,2	K562	blood:

Variant related genes	Relation type
STARD9	TF binding region
ENSG00000260282	Chromatin interaction
ENSG00000137814	Chromatin interaction
ENSG00000261822	Chromatin interaction
ENSG00000260490	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000092531	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1044866	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11541527	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973349	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5009460	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57249373	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57349778	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58122107	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58562675	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58952814	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59058205	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59091063	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60060355	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60168929	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60606292	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60697170	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60839827	1.00[AMR][1000 genomes]
rs61368952	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61474811	0.85[AMR][1000 genomes]
rs6493048	0.80[AFR][1000 genomes]
rs6493049	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493050	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7166633	0.87[AMR][1000 genomes]
rs7172064	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7172955	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173155	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7175059	0.87[AMR][1000 genomes]
rs7178822	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7181938	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402762	0.85[AMR][1000 genomes]
rs73402776	0.85[AMR][1000 genomes]
rs73402796	0.87[AMR][1000 genomes]
rs73404708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404711	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404725	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404729	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404744	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404746	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404754	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73404758	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404768	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404774	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404775	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404793	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73404797	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406503	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406509	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406526	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406531	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73406557	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs768118	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8023948	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8027207	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031383	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8031883	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033555	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033810	1.00[AMR][1000 genomes]
rs8034001	1.00[AMR][1000 genomes]
rs8035877	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8036927	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8037277	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8040624	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv976927	chr15:42862948-42868443	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42855200-42867800	Weak transcription	Aorta	Aorta
2	chr15:42859000-42868000	Weak transcription	Fetal Brain Male	brain
3	chr15:42859400-42867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:42860400-42867800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:42866800-42868000	Active TSS	Brain Germinal Matrix	brain
6	chr15:42867000-42867800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:42867000-42868000	Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr15:42867000-42868000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42867000-42868000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:42867000-42868200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr15:42867000-42868200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr15:42867000-42868200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr15:42867000-42868200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:42867000-42868200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:42867000-42868200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:42867000-42868200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr15:42867000-42868200	Active TSS	Fetal Lung	lung
18	chr15:42867000-42868200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr15:42867000-42868400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr15:42867000-42868400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:42867000-42868400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:42867000-42868400	Active TSS	Brain Angular Gyrus	brain
23	chr15:42867000-42868400	Active TSS	Brain Substantia Nigra	brain
24	chr15:42867000-42868400	Active TSS	A549	lung
25	chr15:42867000-42868600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:42867000-42868600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr15:42867000-42868600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:42867000-42868600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr15:42867000-42868600	Active TSS	HSMMtube	muscle
30	chr15:42867000-42868800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr15:42867000-42868800	Active TSS	Psoas Muscle	Psoas
32	chr15:42867000-42869000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr15:42867000-42869000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:42867000-42869000	Active TSS	Fetal Kidney	kidney
35	chr15:42867000-42869000	Active TSS	Right Atrium	heart
36	chr15:42867200-42867800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:42867200-42868000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr15:42867200-42868000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr15:42867200-42868000	Active TSS	Colonic Mucosa	Colon
40	chr15:42867200-42868000	Active TSS	Placenta Amnion	Placenta Amnion
41	chr15:42867200-42868000	Active TSS	Osteobl	bone
42	chr15:42867200-42868200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:42867200-42868200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:42867200-42868200	Active TSS	Primary T cells from cord blood	blood
45	chr15:42867200-42868200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:42867200-42868200	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr15:42867200-42868200	Active TSS	NHEK	skin
48	chr15:42867200-42868400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:42867200-42868400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:42867200-42868400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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