Variant report

Variant	rs1642927
Chromosome Location	chr15:57251257-57251258
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	chr15:57208582..57210610-chr15:57249153..57251996,2	K562	blood:
2	chr15:57243814..57246675-chr15:57249324..57251467,2	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1015967	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10438332	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11071302	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11071307	1.00[CEU][hapmap]
rs1139006	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630965	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632502	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11632526	0.97[EUR][1000 genomes]
rs11636655	1.00[CEU][hapmap]
rs11856338	0.88[EUR][1000 genomes]
rs12148850	0.91[EUR][1000 genomes]
rs12437976	0.82[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs12440219	0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes]
rs12591367	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12593843	1.00[CEU][hapmap]
rs12595644	0.95[EUR][1000 genomes]
rs12902058	0.82[CEU][hapmap]
rs12906025	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1346880	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs1367491	0.93[EUR][1000 genomes]
rs1625176	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1628974	0.99[EUR][1000 genomes]
rs1631079	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1642925	0.96[EUR][1000 genomes]
rs1642928	0.99[EUR][1000 genomes]
rs1642929	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1642935	0.94[EUR][1000 genomes]
rs1642936	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1642937	0.94[EUR][1000 genomes]
rs1642940	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs1652732	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1652737	0.95[EUR][1000 genomes]
rs1652738	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1652739	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1652740	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1652741	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1657926	1.00[CEU][hapmap]
rs17239222	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17819940	1.00[CEU][hapmap]
rs1820996	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs190039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1963831	0.84[CEU][hapmap]
rs2111892	0.89[EUR][1000 genomes]
rs2126402	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs213148	0.94[EUR][1000 genomes]
rs213152	0.83[EUR][1000 genomes]
rs213160	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs213163	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs213166	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs213168	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2169468	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2252289	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2435905	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs2439921	0.91[EUR][1000 genomes]
rs2439925	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2464427	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2464428	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2470080	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2470081	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2470083	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2470084	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2543675	0.82[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2566840	0.82[CEU][hapmap]
rs2566844	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2566846	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2566856	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2585076	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2585116	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703588	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2733187	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2915176	0.92[EUR][1000 genomes]
rs2920268	0.85[EUR][1000 genomes]
rs2920270	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2920272	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2951897	0.82[EUR][1000 genomes]
rs2951900	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2951902	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2957573	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2957576	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2957578	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs2957592	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2962994	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2962995	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4774246	0.82[CEU][hapmap]
rs55886927	0.89[EUR][1000 genomes]
rs7164742	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs7168945	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs7183392	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs72749478	0.95[EUR][1000 genomes]
rs72749491	0.97[EUR][1000 genomes]
rs7359192	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8029445	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8042190	1.00[CEU][hapmap]
rs9806712	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
2	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:57222800-57255000	Weak transcription	HMEC	breast
4	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:57229400-57255800	Weak transcription	Fetal Stomach	stomach
7	chr15:57232000-57256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:57238400-57256200	Weak transcription	K562	blood
9	chr15:57241000-57255600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:57241200-57251600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:57241200-57254400	Weak transcription	NHLF	lung
12	chr15:57242200-57251400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:57242200-57256000	Weak transcription	Ovary	ovary
14	chr15:57242600-57252000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:57244000-57255800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:57244200-57257800	Weak transcription	Fetal Intestine Small	intestine
17	chr15:57246800-57256000	Weak transcription	Gastric	stomach
18	chr15:57248600-57251800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr15:57248800-57251800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr15:57249000-57252000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:57249200-57251600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:57249200-57252400	Enhancers	Dnd41	blood
23	chr15:57249400-57251400	Weak transcription	HSMM	muscle
24	chr15:57249400-57251600	Weak transcription	Osteobl	bone
25	chr15:57249400-57254600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:57249400-57256000	Weak transcription	Aorta	Aorta
27	chr15:57249800-57251400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:57249800-57251800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr15:57249800-57251800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr15:57249800-57252000	Enhancers	Liver	Liver
31	chr15:57249800-57252200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr15:57250000-57251600	Enhancers	Thymus	Thymus
33	chr15:57250000-57251800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:57250000-57252000	Enhancers	Fetal Thymus	thymus
35	chr15:57250000-57252200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr15:57250000-57252400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr15:57250000-57256200	Weak transcription	Primary B cells from cord blood	blood
38	chr15:57250200-57251600	Enhancers	Brain Substantia Nigra	brain
39	chr15:57250200-57251800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr15:57250200-57251800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:57250200-57251800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:57250200-57251800	Enhancers	Fetal Heart	heart
43	chr15:57250200-57252200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr15:57250200-57252400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:57250400-57251800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr15:57250400-57252000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr15:57250600-57252000	Enhancers	Brain Hippocampus Middle	brain
48	chr15:57250600-57252600	Enhancers	Primary T cells from cord blood	blood
49	chr15:57250600-57253000	Enhancers	GM12878-XiMat	blood
50	chr15:57250600-57254400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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