Variant report

Variant	rs686666
Chromosome Location	chr15:44161550-44161551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44149483..44153961-chr15:44160698..44164757,7	K562	blood:
2	chr15:44152030..44153831-chr15:44160698..44163562,2	K562	blood:

Variant related genes	Relation type
ENSG00000092470	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1053492	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11070410	0.95[CEU][hapmap]
rs11638972	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs1975364	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2467426	0.81[CHB][hapmap]
rs2927085	0.81[CEU][hapmap]
rs2955969	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3087657	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs35866764	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4597285	0.91[ASN][1000 genomes]
rs472385	0.85[AMR][1000 genomes]
rs4924722	0.82[EUR][1000 genomes]
rs524908	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs533143	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs575082	0.95[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs663214	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs667476	0.83[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs688009	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs693919	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs694461	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7175129	0.95[CEU][hapmap]
rs8033995	1.00[CHB][hapmap];0.82[JPT][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	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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs686666	AC011330.5	cis	Thyroid	GTEx
rs686666	ZSCAN29	cis	multi-tissue	Pritchard
rs686666	STRCP1	cis	Whole Blood	GTEx
rs686666	AC011330.5	cis	Artery Tibial	GTEx
rs686666	ZSCAN29	cis	Thyroid	GTEx

Chromatin state (count:106 , 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	chr15:44120600-44164600	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:44120600-44164600	Weak transcription	NHEK	skin
9	chr15:44120600-44165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:44124000-44166000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:44128200-44167800	Weak transcription	Ovary	ovary
13	chr15:44128600-44167800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:44131200-44167600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:44133000-44166000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:44142200-44163800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:44142200-44164600	Weak transcription	Brain Angular Gyrus	brain
18	chr15:44144800-44181000	Weak transcription	HepG2	liver
19	chr15:44146600-44165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:44146600-44165800	Weak transcription	Osteobl	bone
21	chr15:44146800-44181600	Weak transcription	Gastric	stomach
22	chr15:44147600-44172000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:44148200-44166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:44149600-44166200	Weak transcription	A549	lung
25	chr15:44150600-44174600	Strong transcription	Dnd41	blood
26	chr15:44151200-44161600	Weak transcription	Fetal Heart	heart
27	chr15:44151600-44171200	Weak transcription	Placenta	Placenta
28	chr15:44151600-44181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:44152000-44172800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:44152200-44166400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:44152400-44164600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:44152600-44164400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:44152600-44166000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:44152600-44167800	Weak transcription	Aorta	Aorta
35	chr15:44152600-44168000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:44152600-44168600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:44152600-44169600	Weak transcription	Lung	lung
38	chr15:44152600-44180800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:44152800-44166200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr15:44153600-44163400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:44153800-44166000	Weak transcription	NHLF	lung
42	chr15:44153800-44166200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:44153800-44172000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:44155000-44162200	Strong transcription	Fetal Thymus	thymus
45	chr15:44156000-44165000	Weak transcription	Thymus	Thymus
46	chr15:44156200-44166000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:44156400-44162200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:44156400-44166800	Strong transcription	Hela-S3	cervix
49	chr15:44156600-44165400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:44156800-44169600	Weak transcription	NHDF-Ad	bronchial

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