Variant report

Variant	rs2412821
Chromosome Location	chr15:44157164-44157165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11070411	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap]
rs2729494	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2918947	0.88[AMR][1000 genomes]
rs2930529	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3102448	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35267287	0.82[AFR][1000 genomes]
rs3862143	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3986209	0.84[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs495880	0.93[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs514311	0.92[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs541871	0.93[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6493090	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs654276	0.93[CEU][hapmap]
rs678084	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7174260	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7178230	0.84[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	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
2	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
3	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
4	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
5	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
6	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
rs2412821	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44119600-44166000	Weak transcription	Spleen	Spleen
2	chr15:44119600-44169400	Weak transcription	Fetal Intestine Large	intestine
3	chr15:44119600-44172800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
5	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:44119800-44166400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:44120600-44157800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:44120600-44158600	Weak transcription	Colonic Mucosa	Colon
9	chr15:44120600-44159600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:44120600-44161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:44120600-44164600	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:44120600-44164600	Weak transcription	NHEK	skin
13	chr15:44120600-44165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:44121400-44159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:44121400-44160600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:44124000-44166000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:44128200-44167800	Weak transcription	Ovary	ovary
19	chr15:44128600-44167800	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:44129200-44161200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:44131200-44167600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:44133000-44166000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:44135400-44157800	Weak transcription	Fetal Kidney	kidney
24	chr15:44137800-44160200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:44142200-44163800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:44142200-44164600	Weak transcription	Brain Angular Gyrus	brain
27	chr15:44144000-44160400	Weak transcription	HSMM	muscle
28	chr15:44144800-44181000	Weak transcription	HepG2	liver
29	chr15:44146600-44158200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:44146600-44165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:44146600-44165800	Weak transcription	Osteobl	bone
32	chr15:44146800-44158000	Weak transcription	Brain Anterior Caudate	brain
33	chr15:44146800-44181600	Weak transcription	Gastric	stomach
34	chr15:44147600-44172000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:44147800-44160000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:44148000-44160400	Weak transcription	Liver	Liver
37	chr15:44148200-44166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:44149600-44166200	Weak transcription	A549	lung
39	chr15:44150600-44174600	Strong transcription	Dnd41	blood
40	chr15:44151200-44161600	Weak transcription	Fetal Heart	heart
41	chr15:44151600-44157800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:44151600-44171200	Weak transcription	Placenta	Placenta
43	chr15:44151600-44181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:44152000-44161000	Weak transcription	NH-A	brain
45	chr15:44152000-44172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:44152200-44158000	Weak transcription	Primary B cells from cord blood	blood
47	chr15:44152200-44161400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:44152200-44166400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:44152400-44159800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr15:44152400-44160400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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