Variant report

Variant	rs73406505
Chromosome Location	chr15:42839924-42839925
allele	C/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	E2F4	chr15:42839643-42839975	MCF10A-Er-Src	breast:	n/a	n/a
2	HCFC1	chr15:42839443-42841677	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr15:42839844-42841634	IMR90	lung:	n/a	chr15:42840251-42840266

No.	Distal block	Cell Line	Cell type
1	chr15:42565305..42567163-chr15:42839364..42842481,3	K562	blood:
2	chr15:42838345..42842657-chr15:42865696..42868936,4	MCF-7	breast:
3	chr15:42781650..42784246-chr15:42838736..42840293,2	MCF-7	breast:
4	chr15:42837304..42838910-chr15:42839465..42842272,2	MCF-7	breast:
5	chr15:42838709..42841070-chr15:42866779..42868984,2	MCF-7	breast:

Variant related genes	Relation type
HAUS2	TF binding region
LRRC57	TF binding region
ENSG00000092531	Chromatin interaction
ENSG00000214013	Chromatin interaction
ENSG00000159433	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000103978	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]
rs73406509	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:42817400-42840200	Weak transcription	Pancreas	Pancrea
3	chr15:42822200-42840200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:42822800-42840000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:42823400-42840200	Weak transcription	Psoas Muscle	Psoas
6	chr15:42824000-42840200	Weak transcription	Small Intestine	intestine
7	chr15:42831600-42840200	Weak transcription	Gastric	stomach
8	chr15:42837000-42840000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:42837000-42840200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:42837000-42840200	Weak transcription	Lung	lung
11	chr15:42837000-42840200	Weak transcription	Spleen	Spleen
12	chr15:42837400-42840000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr15:42837400-42840000	Weak transcription	Aorta	Aorta
14	chr15:42837400-42840200	Weak transcription	Esophagus	oesophagus
15	chr15:42837600-42840000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr15:42837600-42840200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:42838000-42840000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:42838000-42840200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr15:42838200-42840000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:42838400-42840200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr15:42838600-42840200	Flanking Active TSS	HMEC	breast
22	chr15:42838600-42840400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:42838800-42840000	Enhancers	Rectal Smooth Muscle	rectum
24	chr15:42839000-42840000	Enhancers	Thymus	Thymus
25	chr15:42839200-42840000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:42839200-42840000	Enhancers	Primary B cells from cord blood	blood
27	chr15:42839200-42840000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr15:42839200-42840000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr15:42839200-42840000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr15:42839200-42840000	Enhancers	Fetal Intestine Small	intestine
31	chr15:42839200-42840000	Enhancers	Fetal Stomach	stomach
32	chr15:42839200-42840200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:42839200-42840200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr15:42839200-42840200	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr15:42839200-42840200	Flanking Active TSS	NHLF	lung
36	chr15:42839200-42840400	Flanking Active TSS	Hela-S3	cervix
37	chr15:42839400-42840000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:42839400-42840000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:42839400-42840000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr15:42839400-42840000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:42839400-42840000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:42839400-42840000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:42839400-42840000	Enhancers	Liver	Liver
44	chr15:42839400-42840000	Enhancers	Brain Substantia Nigra	brain
45	chr15:42839400-42840000	Enhancers	Fetal Lung	lung
46	chr15:42839400-42840000	Enhancers	Placenta	Placenta
47	chr15:42839400-42840000	Enhancers	Left Ventricle	heart
48	chr15:42839400-42840000	Enhancers	Stomach Mucosa	stomach
49	chr15:42839400-42840000	Flanking Active TSS	NHDF-Ad	bronchial
50	chr15:42839400-42840200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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