Variant report

Variant	rs1642937
Chromosome Location	chr15:57269553-57269554
allele	A/G
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
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1015967	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10438332	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071302	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071307	0.80[ASN][1000 genomes]
rs1139006	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630965	0.88[EUR][1000 genomes]
rs11632502	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632526	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636655	0.81[ASN][1000 genomes]
rs11856338	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148850	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12591367	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595644	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902058	0.86[AMR][1000 genomes]
rs12906025	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1346880	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1367491	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1625176	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628974	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1631079	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642925	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642927	0.94[EUR][1000 genomes]
rs1642928	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642929	0.95[EUR][1000 genomes]
rs1642935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642936	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642940	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652732	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652737	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1652738	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1652739	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652740	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652741	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657926	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs169893	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17239222	0.82[EUR][1000 genomes]
rs17819940	0.80[ASN][1000 genomes]
rs1820996	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs190039	0.89[EUR][1000 genomes]
rs2111890	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2111892	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126402	0.82[EUR][1000 genomes]
rs213148	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213152	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs213160	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs213163	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs213166	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213168	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163370	0.81[AMR][1000 genomes]
rs2169468	0.82[EUR][1000 genomes]
rs2252289	0.82[EUR][1000 genomes]
rs2435905	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439921	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439925	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2464427	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2464428	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2470080	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470081	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470083	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2470084	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2543675	0.82[EUR][1000 genomes]
rs2566840	0.81[AMR][1000 genomes]
rs2566844	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566846	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2566856	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2585076	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2585116	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703588	0.83[EUR][1000 genomes]
rs2733187	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28637136	0.82[ASN][1000 genomes]
rs2915176	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920268	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2920270	0.82[EUR][1000 genomes]
rs2920272	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2951896	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2951897	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2951900	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2951902	0.82[EUR][1000 genomes]
rs2957573	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957576	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2957578	0.83[EUR][1000 genomes]
rs2957592	0.81[EUR][1000 genomes]
rs2962994	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2962995	0.82[EUR][1000 genomes]
rs4774246	0.86[AMR][1000 genomes]
rs4774247	0.83[ASN][1000 genomes]
rs55886927	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7162730	0.80[AMR][1000 genomes]
rs7168945	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7183392	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72731924	0.81[ASN][1000 genomes]
rs72749478	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72749491	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359192	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029445	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9806712	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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:65 , 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	chr15:57261200-57272800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57261400-57272000	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:57262000-57269600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:57262200-57270800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:57263800-57271000	Weak transcription	Hela-S3	cervix
13	chr15:57263800-57272400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:57263800-57276000	Weak transcription	Lung	lung
15	chr15:57264200-57270600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:57264200-57270800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:57264200-57272600	Weak transcription	Thymus	Thymus
18	chr15:57264200-57272800	Weak transcription	Right Atrium	heart
19	chr15:57264200-57272800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:57264800-57275000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:57264800-57275200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:57265000-57269600	Weak transcription	Brain Anterior Caudate	brain
23	chr15:57265000-57272800	Weak transcription	Brain Angular Gyrus	brain
24	chr15:57265200-57269600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:57265400-57277000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:57265600-57269600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:57265600-57269600	Weak transcription	Fetal Brain Male	brain
28	chr15:57265600-57270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:57265600-57271200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:57265800-57271000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:57265800-57271000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:57266200-57270800	Weak transcription	NHLF	lung
33	chr15:57266200-57271000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:57266200-57271000	Weak transcription	NHDF-Ad	bronchial
35	chr15:57266200-57271600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:57266200-57272000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:57266200-57272200	Weak transcription	Small Intestine	intestine
38	chr15:57266200-57274200	Weak transcription	Liver	Liver
39	chr15:57266400-57270000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:57266400-57270800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:57266400-57271000	Weak transcription	K562	blood
42	chr15:57266400-57272800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr15:57266600-57270800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr15:57266600-57271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:57266600-57272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:57267000-57270800	Weak transcription	Primary T cells from cord blood	blood
47	chr15:57267000-57273200	Weak transcription	Dnd41	blood
48	chr15:57267000-57273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:57267000-57274600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:57267400-57274000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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