Variant report

Variant	rs528764
Chromosome Location	chr15:44130848-44130849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	15:43792489-43802874..15:44128499-44135043	GM12878	blood:
2	chr15:44127360..44129810-chr15:44129920..44131455,2	K562	blood:
3	15:44080886-44089111..15:44128499-44135043	GM12878	blood:
4	15:44092692-44100030..15:44128499-44135043	GM12878	blood:
5	15:43782117-43785993..15:44128499-44135043	GM12878	blood:
6	chr15:44130808..44133244-chr15:44134272..44137291,3	K562	blood:

Variant related genes	Relation type
ENSG00000242028	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000067369	Chromatin interaction
ENSG00000221792	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2412821	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2918943	1.00[YRI][hapmap]
rs2918947	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2930529	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3102448	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35267287	0.93[AFR][1000 genomes]
rs35822148	0.89[EUR][1000 genomes]
rs3862143	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes]
rs3986209	0.89[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs514311	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs541871	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018940	0.84[EUR][1000 genomes]
rs62018944	0.81[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174260	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7178230	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
7	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
8	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
10	nsv511550	chr15:44120559-44148142	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs528764	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44117400-44150200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:44119600-44134400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:44119600-44135200	Weak transcription	Lung	lung
4	chr15:44119600-44142000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:44119600-44143200	Weak transcription	Aorta	Aorta
6	chr15:44119600-44143400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:44119600-44150600	Weak transcription	Esophagus	oesophagus
8	chr15:44119600-44151000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:44119600-44156400	Weak transcription	Pancreas	Pancrea
10	chr15:44119600-44166000	Weak transcription	Spleen	Spleen
11	chr15:44119600-44169400	Weak transcription	Fetal Intestine Large	intestine
12	chr15:44119600-44172800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
14	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:44119800-44144400	Weak transcription	Right Ventricle	heart
16	chr15:44119800-44166400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:44120200-44150800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:44120400-44143000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:44120600-44133800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:44120600-44134400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:44120600-44137800	Weak transcription	NH-A	brain
22	chr15:44120600-44138200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:44120600-44140200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:44120600-44143200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:44120600-44143200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:44120600-44149200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr15:44120600-44150800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:44120600-44150800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:44120600-44156600	Weak transcription	Fetal Brain Male	brain
30	chr15:44120600-44157800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:44120600-44158600	Weak transcription	Colonic Mucosa	Colon
32	chr15:44120600-44159600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:44120600-44161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:44120600-44164600	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:44120600-44164600	Weak transcription	NHEK	skin
36	chr15:44120600-44165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:44121000-44134800	Weak transcription	Fetal Kidney	kidney
38	chr15:44121000-44137400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:44121000-44137400	Weak transcription	Osteobl	bone
40	chr15:44121000-44143000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:44121000-44143200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:44121000-44143200	Weak transcription	HSMM	muscle
43	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:44121400-44159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:44121400-44160600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:44121600-44150800	Weak transcription	Fetal Heart	heart
47	chr15:44121600-44151200	Weak transcription	NHLF	lung
48	chr15:44122000-44134600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:44122000-44157000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:44122400-44143200	Weak transcription	Placenta	Placenta

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