Variant report

Variant	rs16986864
Chromosome Location	chr22:29350911-29350912
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29344969..29347183-chr22:29349320..29351089,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1222	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs13056243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13058031	0.94[CEU][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs13058453	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs132539	0.84[CHD][hapmap];0.80[GIH][hapmap]
rs16986825	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16986838	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16986861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267131	0.94[CEU][hapmap]
rs2301428	0.94[CEU][hapmap]
rs28360615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34578331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5752797	0.89[CEU][hapmap]
rs5752803	0.94[CEU][hapmap]
rs5752811	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs5762780	0.87[CEU][hapmap]
rs5762799	0.89[CEU][hapmap]
rs5762814	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs5762816	0.94[CEU][hapmap];0.81[TSI][hapmap]
rs739196	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs916332	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16986864	MN1	cis	cerebellum	SCAN
rs16986864	FLJ33814	cis	multi-tissue	Pritchard
rs16986864	SUSD2	cis	parietal	SCAN
rs16986864	PIWIL3	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29339800-29352600	Weak transcription	Stomach Mucosa	stomach
2	chr22:29345800-29351200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr22:29346400-29353800	Weak transcription	NHEK	skin
4	chr22:29346400-29357400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr22:29346600-29352800	Weak transcription	Brain Substantia Nigra	brain
6	chr22:29347600-29356200	Weak transcription	Brain Germinal Matrix	brain
7	chr22:29348000-29352400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr22:29348200-29351400	Enhancers	HepG2	liver
9	chr22:29348200-29351800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:29348200-29351800	Weak transcription	Lung	lung
11	chr22:29348200-29352000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr22:29348200-29353800	Enhancers	Colon Smooth Muscle	Colon
13	chr22:29348200-29365000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr22:29348400-29351400	Weak transcription	Spleen	Spleen
15	chr22:29348400-29352400	Weak transcription	Brain Angular Gyrus	brain
16	chr22:29348400-29352600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr22:29348600-29351800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr22:29348800-29360400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr22:29349000-29352000	Weak transcription	Brain Anterior Caudate	brain
20	chr22:29349200-29352000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:29349200-29352000	Weak transcription	Brain Hippocampus Middle	brain
22	chr22:29349200-29352200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr22:29349200-29352400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr22:29349200-29356800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:29349200-29365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr22:29349200-29371800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr22:29349200-29371800	Weak transcription	HSMM	muscle
28	chr22:29349400-29351400	Weak transcription	Gastric	stomach
29	chr22:29349400-29351400	Weak transcription	Right Atrium	heart
30	chr22:29349400-29351800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr22:29349400-29351800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:29349400-29352600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr22:29349400-29354400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr22:29349400-29354600	Weak transcription	Adipose Nuclei	Adipose
35	chr22:29349400-29357200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr22:29349400-29357400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr22:29349400-29357400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr22:29349600-29351800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:29349600-29352400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr22:29349600-29352400	Weak transcription	Hela-S3	cervix
41	chr22:29349600-29352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr22:29349600-29354400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr22:29349600-29354400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr22:29349600-29354800	Weak transcription	A549	lung
45	chr22:29349600-29357200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr22:29349600-29359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr22:29349800-29351800	Weak transcription	Right Ventricle	heart
48	chr22:29349800-29360400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr22:29350000-29351800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:29350000-29351800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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