Variant report

Variant	rs2439924
Chromosome Location	chr15:57269055-57269056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57210623..57212439-chr15:57268070..57269704,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1652733	1.00[YRI][hapmap]
rs2243575	1.00[AMR][1000 genomes]
rs2435894	1.00[AMR][1000 genomes]
rs2435898	0.94[AFR][1000 genomes]
rs2435899	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435901	0.81[AFR][1000 genomes]
rs2435904	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2439923	0.81[AFR][1000 genomes]
rs2566841	0.88[AFR][1000 genomes]
rs2566847	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2566852	0.81[AFR][1000 genomes]
rs2585074	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2585079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585085	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585095	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585101	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2585109	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2585113	1.00[AMR][1000 genomes]
rs2585122	1.00[YRI][hapmap]
rs2593245	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2593247	0.93[AFR][1000 genomes]
rs2593253	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2615234	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2615239	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2615245	0.93[AFR][1000 genomes]
rs2615247	1.00[AMR][1000 genomes]
rs2703581	1.00[AMR][1000 genomes]
rs2703585	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2703603	0.81[AFR][1000 genomes]
rs2703606	0.81[AFR][1000 genomes]
rs2703611	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703615	0.87[AFR][1000 genomes]
rs2703617	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2703621	1.00[AMR][1000 genomes]
rs2703622	0.81[AFR][1000 genomes]
rs2733173	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2733175	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2733184	1.00[AMR][1000 genomes]
rs2733308	1.00[AMR][1000 genomes]
rs2733338	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2920271	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
3	chr15:57260000-57272200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:57260000-57272400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:57261000-57269400	Weak transcription	Psoas Muscle	Psoas
6	chr15:57261200-57272800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:57261400-57272000	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:57262000-57269400	Weak transcription	Ovary	ovary
11	chr15:57262000-57269600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:57262200-57270800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:57263800-57271000	Weak transcription	Hela-S3	cervix
15	chr15:57263800-57272400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:57263800-57276000	Weak transcription	Lung	lung
17	chr15:57264200-57270600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:57264200-57270800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:57264200-57272600	Weak transcription	Thymus	Thymus
20	chr15:57264200-57272800	Weak transcription	Right Atrium	heart
21	chr15:57264200-57272800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:57264600-57269400	Weak transcription	Left Ventricle	heart
23	chr15:57264800-57275000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:57264800-57275200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:57265000-57269600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:57265000-57272800	Weak transcription	Brain Angular Gyrus	brain
27	chr15:57265200-57269600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:57265400-57277000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:57265600-57269600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:57265600-57269600	Weak transcription	Fetal Brain Male	brain
31	chr15:57265600-57270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:57265600-57271200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:57265800-57271000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:57265800-57271000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:57266200-57269200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:57266200-57270800	Weak transcription	NHLF	lung
37	chr15:57266200-57271000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:57266200-57271000	Weak transcription	NHDF-Ad	bronchial
39	chr15:57266200-57271600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:57266200-57272000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:57266200-57272200	Weak transcription	Small Intestine	intestine
42	chr15:57266200-57274200	Weak transcription	Liver	Liver
43	chr15:57266400-57270000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:57266400-57270800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:57266400-57271000	Weak transcription	K562	blood
46	chr15:57266400-57272800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr15:57266600-57270800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr15:57266600-57271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:57266600-57272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:57267000-57270800	Weak transcription	Primary T cells from cord blood	blood

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