Variant report

Variant	rs933860
Chromosome Location	chr15:52965468-52965469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52960932..52963378-chr15:52964421..52966034,2	K562	blood:
2	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:
3	chr15:52964942..52967730-chr15:52969807..52971860,2	K562	blood:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1080731	1.00[CHB][hapmap]
rs10851521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070908	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11070909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11853917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855616	1.00[CHB][hapmap]
rs11857150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858743	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12232257	0.91[JPT][hapmap]
rs12898644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap]
rs12914047	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12914502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13329393	1.00[CHB][hapmap]
rs17614559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap]
rs1863512	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2288271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2414160	1.00[CHB][hapmap]
rs2414161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs2414163	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414167	1.00[CHB][hapmap]
rs34431049	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4390542	1.00[CHB][hapmap]
rs4548810	0.95[CEU][hapmap];0.89[CHB][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs4774634	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4774636	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4776063	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs4776065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4776068	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62023352	0.82[ASN][1000 genomes]
rs7167494	1.00[CHB][hapmap]
rs8026800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030141	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv457140	chr15:52901433-52968746	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52871800-52967600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:52944200-52965800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
6	chr15:52945000-52968600	Weak transcription	HepG2	liver
7	chr15:52946000-52968200	Weak transcription	Fetal Heart	heart
8	chr15:52946000-52968600	Weak transcription	Stomach Mucosa	stomach
9	chr15:52949200-52965600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:52949400-52966400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr15:52950400-52965800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:52950400-52965800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:52950400-52969400	Weak transcription	A549	lung
14	chr15:52950800-52968400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:52951000-52965600	Strong transcription	Adipose Nuclei	Adipose
16	chr15:52951000-52970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:52952000-52967400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:52952000-52968000	Strong transcription	Fetal Thymus	thymus
19	chr15:52952200-52967800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:52952400-52966200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:52953200-52965800	Strong transcription	Primary hematopoietic stem cells	blood
22	chr15:52953200-52967800	Weak transcription	Fetal Intestine Small	intestine
23	chr15:52957000-52966400	Weak transcription	Esophagus	oesophagus
24	chr15:52957400-52967400	Weak transcription	Right Atrium	heart
25	chr15:52957400-52970000	Weak transcription	Colonic Mucosa	Colon
26	chr15:52957400-52970000	Weak transcription	Lung	lung
27	chr15:52958000-52966800	Strong transcription	NHDF-Ad	bronchial
28	chr15:52958200-52966400	Strong transcription	Liver	Liver
29	chr15:52959200-52967200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:52960000-52969000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:52960400-52967600	Weak transcription	Ovary	ovary
32	chr15:52960400-52969600	Weak transcription	HMEC	breast
33	chr15:52960600-52965600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:52960600-52969400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:52960600-52969400	Weak transcription	NHEK	skin
36	chr15:52960600-52970000	Weak transcription	Small Intestine	intestine
37	chr15:52961600-52965800	Strong transcription	Primary T cells from cord blood	blood
38	chr15:52961600-52966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:52961600-52969000	Strong transcription	Osteobl	bone
40	chr15:52962000-52965800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:52962000-52965800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:52962000-52967600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:52962200-52967800	Strong transcription	Fetal Lung	lung
44	chr15:52962200-52967800	Strong transcription	NH-A	brain
45	chr15:52962200-52969800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:52962400-52965600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:52962400-52969400	Weak transcription	Fetal Stomach	stomach
48	chr15:52962600-52965600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr15:52962600-52966800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:52962600-52967800	Weak transcription	Pancreas	Pancrea

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