Variant report

Variant	rs10163069
Chromosome Location	chr15:44047570-44047571
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	15:43792489-43802874..15:44044200-44049293	Hela-S3	cervix:
2	chr15:44045694..44048584-chr15:44091714..44093995,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067369	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000242028	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11070411	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12443084	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap]
rs17795279	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs2412821	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2918947	0.82[EUR][1000 genomes]
rs2930529	0.94[EUR][1000 genomes]
rs2930530	0.81[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[LWK][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes]
rs3102448	0.87[EUR][1000 genomes]
rs3110081	0.86[EUR][1000 genomes]
rs35822148	0.86[EUR][1000 genomes]
rs3844075	0.85[YRI][hapmap];0.92[AFR][1000 genomes]
rs3862143	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3986209	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];0.84[GIH][hapmap];0.80[LWK][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs62018940	0.90[EUR][1000 genomes]
rs62018944	0.88[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes]
rs7174260	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7178230	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs8038068	1.00[CEU][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10163069	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44039200-44049400	Weak transcription	Spleen	Spleen
2	chr15:44039600-44052000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:44039600-44055400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:44039800-44048800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:44040200-44048200	Weak transcription	Fetal Kidney	kidney
6	chr15:44040200-44049200	Weak transcription	Esophagus	oesophagus
7	chr15:44040200-44056000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:44040200-44062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:44040800-44055600	Weak transcription	Psoas Muscle	Psoas
10	chr15:44040800-44055800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:44041000-44068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:44042000-44066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:44042000-44066800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:44042000-44067000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:44042200-44049600	Weak transcription	Gastric	stomach
16	chr15:44042200-44055400	Weak transcription	Aorta	Aorta
17	chr15:44042200-44067000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:44042400-44049400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:44042600-44048400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:44042600-44049400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:44042600-44053400	Weak transcription	Fetal Brain Male	brain
22	chr15:44042600-44066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:44042800-44048600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:44043000-44066800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:44043400-44049200	Strong transcription	NHDF-Ad	bronchial
26	chr15:44043400-44055000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:44043400-44063200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:44043400-44066600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:44043400-44066600	Strong transcription	Fetal Thymus	thymus
30	chr15:44043400-44066800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:44043400-44066800	Strong transcription	Placenta	Placenta
32	chr15:44043400-44067000	Strong transcription	Osteobl	bone
33	chr15:44043400-44067200	Strong transcription	HSMM	muscle
34	chr15:44043600-44053200	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr15:44043600-44063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:44043600-44063800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr15:44043600-44066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:44043600-44066800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr15:44043800-44049400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:44043800-44050600	Strong transcription	HSMMtube	muscle
41	chr15:44043800-44066800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:44044000-44048200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:44044000-44049400	Strong transcription	NH-A	brain
44	chr15:44044000-44052000	Strong transcription	NHEK	skin
45	chr15:44044000-44052600	Strong transcription	K562	blood
46	chr15:44044000-44056800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr15:44044000-44063800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:44044000-44063800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:44044000-44066600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:44044000-44067000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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