Variant report

Variant	rs16922990
Chromosome Location	chr8:58983976-58983977
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	chr8:58909602..58910570-chr8:58983968..58984807,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10093645	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11998684	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12155558	0.85[ASN][1000 genomes]
rs12156321	0.85[CHB][hapmap]
rs13263290	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs13263507	1.00[CHB][hapmap]
rs13268233	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13273891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13277246	1.00[CHB][hapmap]
rs16922941	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs17175390	0.85[CHB][hapmap]
rs17175804	0.85[CHB][hapmap]
rs17175965	0.85[CHB][hapmap]
rs17254739	0.85[CHB][hapmap]
rs35350559	0.85[ASN][1000 genomes]
rs35979674	0.85[ASN][1000 genomes]
rs6984700	0.85[CHB][hapmap]
rs6988260	0.85[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6991555	0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6997924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7000317	0.85[ASN][1000 genomes]
rs7010934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7823853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7835676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831324	chr8:58844151-59045309	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1803360	chr8:58976889-58986166	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16922990	IMPAD1	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:58935600-58988800	Weak transcription	Aorta	Aorta
2	chr8:58952200-58986400	Weak transcription	Adipose Nuclei	Adipose
3	chr8:58979400-58999600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:58979600-58988600	Weak transcription	Lung	lung
5	chr8:58980200-58984000	Weak transcription	Pancreas	Pancrea
6	chr8:58980200-58988800	Weak transcription	Placenta	Placenta
7	chr8:58980400-58991400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr8:58980400-58994400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr8:58980600-58984000	Weak transcription	Stomach Mucosa	stomach
10	chr8:58980600-58988800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr8:58980600-58999600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:58980800-58984400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr8:58980800-58989200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:58980800-58991600	Weak transcription	Osteobl	bone
15	chr8:58980800-58992000	Weak transcription	Fetal Intestine Small	intestine
16	chr8:58981200-58984000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:58981200-58988800	Weak transcription	Ovary	ovary
18	chr8:58981200-58989600	Weak transcription	NHLF	lung
19	chr8:58981400-58985800	Weak transcription	Liver	Liver
20	chr8:58982000-58984000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:58982200-58986600	Weak transcription	HepG2	liver
22	chr8:58982400-58984600	Active TSS	Brain Angular Gyrus	brain
23	chr8:58982600-58984000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr8:58982600-58984200	Active TSS	Fetal Brain Female	brain
25	chr8:58982600-58984400	Active TSS	Brain Cingulate Gyrus	brain
26	chr8:58982600-58984400	Enhancers	Colon Smooth Muscle	Colon
27	chr8:58982600-58984400	Active TSS	Psoas Muscle	Psoas
28	chr8:58982600-58984400	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr8:58982600-58984600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:58982600-58984800	Active TSS	Left Ventricle	heart
31	chr8:58982800-58984400	Active TSS	Fetal Muscle Trunk	muscle
32	chr8:58982800-58984600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr8:58982800-58984600	Active TSS	Right Atrium	heart
34	chr8:58982800-58984600	Enhancers	NHDF-Ad	bronchial
35	chr8:58982800-58985000	Active TSS	Right Ventricle	heart
36	chr8:58983000-58984000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr8:58983000-58984400	Enhancers	Fetal Stomach	stomach
38	chr8:58983000-58984600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr8:58983000-58984600	Enhancers	HSMMtube	muscle
40	chr8:58983000-58985000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr8:58983000-58985000	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr8:58983000-58986400	Enhancers	Fetal Lung	lung
43	chr8:58983000-58986800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr8:58983000-58989800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:58983200-58984400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:58983200-58984600	Active TSS	Brain Anterior Caudate	brain
47	chr8:58983200-58984600	Enhancers	Brain Substantia Nigra	brain
48	chr8:58983200-58984600	Enhancers	Rectal Smooth Muscle	rectum
49	chr8:58983200-58984800	Enhancers	HSMM	muscle
50	chr8:58983200-58986800	Weak transcription	Spleen	Spleen

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