Variant report

Variant	rs2930529
Chromosome Location	chr15:44111665-44111666
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	chr15:44082965..44094882-chr15:44108427..44121402,26	K562	blood:

Variant related genes	Relation type
ENSG00000184716	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000140264	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10163069	0.94[EUR][1000 genomes]
rs11070411	0.93[EUR][1000 genomes]
rs12443084	0.84[EUR][1000 genomes]
rs2412821	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2729494	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28410121	0.93[EUR][1000 genomes]
rs2918947	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2930530	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930531	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3102448	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3110081	0.81[EUR][1000 genomes]
rs35822148	0.92[EUR][1000 genomes]
rs3862143	0.92[EUR][1000 genomes]
rs3986209	0.94[EUR][1000 genomes]
rs4644832	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4923964	0.87[EUR][1000 genomes]
rs4923965	0.96[EUR][1000 genomes]
rs495880	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs514311	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs528764	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs541871	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62018940	0.85[EUR][1000 genomes]
rs62018944	0.82[EUR][1000 genomes]
rs6493090	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs654276	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678084	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7174260	0.93[EUR][1000 genomes]
rs7178230	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2930529	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44093600-44116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:44093600-44116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44093800-44112800	Strong transcription	Thymus	Thymus
4	chr15:44093800-44113800	Weak transcription	Stomach Mucosa	stomach
5	chr15:44093800-44115800	Weak transcription	Right Atrium	heart
6	chr15:44094000-44113200	Strong transcription	Fetal Muscle Leg	muscle
7	chr15:44094000-44113400	Strong transcription	Fetal Stomach	stomach
8	chr15:44094000-44114600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:44094000-44114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:44094200-44113000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:44094200-44113200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:44094400-44113200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:44094400-44113200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:44101000-44113200	Strong transcription	Fetal Intestine Small	intestine
15	chr15:44105000-44115800	Weak transcription	Psoas Muscle	Psoas
16	chr15:44106800-44112200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:44106800-44113800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:44106800-44115600	Weak transcription	Right Ventricle	heart
19	chr15:44107000-44112000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:44107200-44116000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:44107400-44112800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:44107400-44115600	Weak transcription	Fetal Heart	heart
23	chr15:44107600-44114200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:44107600-44115400	Weak transcription	Aorta	Aorta
25	chr15:44107800-44112400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:44107800-44113800	Weak transcription	Fetal Brain Male	brain
27	chr15:44107800-44114200	Weak transcription	Esophagus	oesophagus
28	chr15:44107800-44115800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:44107800-44115800	Weak transcription	Gastric	stomach
30	chr15:44108000-44112000	Weak transcription	Pancreas	Pancrea
31	chr15:44108000-44115800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:44108200-44113000	Weak transcription	Small Intestine	intestine
33	chr15:44109400-44115400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:44109800-44114200	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:44109800-44114600	Weak transcription	Lung	lung
36	chr15:44109800-44114600	Weak transcription	Ovary	ovary
37	chr15:44109800-44114800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:44109800-44115600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:44109800-44115800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:44109800-44115800	Weak transcription	HSMMtube	muscle
41	chr15:44109800-44116000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:44110000-44112000	Weak transcription	Spleen	Spleen
43	chr15:44110000-44112400	Weak transcription	Fetal Brain Female	brain
44	chr15:44110000-44112400	Weak transcription	Dnd41	blood
45	chr15:44110000-44112400	Weak transcription	NHEK	skin
46	chr15:44110000-44112600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:44110000-44113600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:44110000-44113600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr15:44110000-44113800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:44110000-44113800	Weak transcription	Muscle Satellite Cultured Cells	--

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