Variant report

Variant	rs1642929
Chromosome Location	chr15:57254842-57254843
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57254284..57256820-chr15:57279086..57281932,2	K562	blood:
2	chr15:57253721..57256073-chr15:57262899..57264820,2	K562	blood:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1015967	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10438332	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11071302	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11071307	1.00[CEU][hapmap]
rs1139006	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11630965	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632502	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11632526	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11636655	1.00[CEU][hapmap]
rs11856338	0.89[EUR][1000 genomes]
rs12148850	0.92[EUR][1000 genomes]
rs12437976	0.84[CEU][hapmap]
rs12591367	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12593843	1.00[CEU][hapmap]
rs12595644	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12902058	0.85[CEU][hapmap]
rs12906025	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1346880	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1367491	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1625176	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1628974	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1631079	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1642925	0.96[EUR][1000 genomes]
rs1642927	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1642928	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1642935	0.95[EUR][1000 genomes]
rs1642936	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1642937	0.95[EUR][1000 genomes]
rs1642940	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1652732	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1652737	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1652738	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1652739	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1652740	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1652741	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1657926	1.00[CEU][hapmap]
rs16977165	0.86[YRI][hapmap]
rs169893	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17239222	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17819940	1.00[CEU][hapmap]
rs1820996	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs190039	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2111892	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2126402	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs213148	0.95[EUR][1000 genomes]
rs213152	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs213160	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs213163	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs213166	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs213168	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2169468	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2252289	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2435905	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2439921	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2439925	0.98[EUR][1000 genomes]
rs2464427	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2464428	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2470080	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2470081	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2470083	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2470084	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2543675	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2566840	0.85[CEU][hapmap]
rs2566844	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2566846	0.98[EUR][1000 genomes]
rs2566856	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2585076	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2585116	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2703588	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2733187	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2915176	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2920268	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2920270	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2920272	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2951897	0.83[EUR][1000 genomes]
rs2951900	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2951902	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2957573	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2957576	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2957578	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2957592	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2962994	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2962995	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4774246	0.84[CEU][hapmap]
rs55886927	0.90[EUR][1000 genomes]
rs7168945	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs7183392	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs72749478	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72749491	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7359192	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8029445	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8042190	1.00[CEU][hapmap]
rs9806712	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[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:83 , 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	chr15:57242200-57256000	Weak transcription	Ovary	ovary
11	chr15:57244000-57255800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:57244200-57257800	Weak transcription	Fetal Intestine Small	intestine
13	chr15:57246800-57256000	Weak transcription	Gastric	stomach
14	chr15:57249400-57256000	Weak transcription	Aorta	Aorta
15	chr15:57250000-57256200	Weak transcription	Primary B cells from cord blood	blood
16	chr15:57250600-57256000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:57251000-57256000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:57251000-57256000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:57251000-57256000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:57251000-57256000	Weak transcription	Right Ventricle	heart
21	chr15:57251000-57259200	Weak transcription	Right Atrium	heart
22	chr15:57251000-57260600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:57251000-57261000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:57251600-57255400	Weak transcription	Thymus	Thymus
25	chr15:57251800-57255000	Weak transcription	Fetal Lung	lung
26	chr15:57251800-57255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:57251800-57255400	Weak transcription	Fetal Heart	heart
28	chr15:57251800-57255400	Weak transcription	NH-A	brain
29	chr15:57251800-57255600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:57251800-57255800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:57251800-57256000	Weak transcription	Left Ventricle	heart
32	chr15:57251800-57256000	Weak transcription	NHEK	skin
33	chr15:57251800-57256200	Weak transcription	HSMM	muscle
34	chr15:57251800-57260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:57252000-57255400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:57252200-57255400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:57252400-57255600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:57252400-57256000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:57252600-57255600	Weak transcription	Liver	Liver
40	chr15:57252600-57255600	Weak transcription	Osteobl	bone
41	chr15:57252600-57256200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:57252800-57255000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:57252800-57255400	Weak transcription	Brain Anterior Caudate	brain
44	chr15:57253000-57255400	Weak transcription	Fetal Thymus	thymus
45	chr15:57253000-57256000	Weak transcription	Psoas Muscle	Psoas
46	chr15:57253400-57256800	Enhancers	Dnd41	blood
47	chr15:57253800-57259000	Enhancers	A549	lung
48	chr15:57254200-57258000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr15:57254400-57255000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr15:57254400-57255200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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