Variant report

Variant	rs9922086
Chromosome Location	chr16:81393779-81393780
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81383148..81385545-chr16:81392228..81393916,3	MCF-7	breast:
2	chr16:81346954..81352914-chr16:81389410..81396228,9	MCF-7	breast:
3	chr16:81388209..81391799-chr16:81392393..81395438,3	MCF-7	breast:
4	chr16:81392614..81395865-chr16:81398430..81401321,3	K562	blood:
5	chr16:81380543..81383435-chr16:81390394..81393830,4	K562	blood:

Variant related genes	Relation type
ENSG00000261609	Chromatin interaction
ENSG00000260495	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12103052	0.92[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12448813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12920172	0.81[CHD][hapmap]
rs12921222	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12925218	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12927652	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12929924	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12933277	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12934500	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1564116	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16955063	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1820260	0.92[CEU][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35151165	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888145	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4889309	0.92[CEU][hapmap]
rs6564872	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7194094	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7199407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199797	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203482	0.96[CEU][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7203835	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs729181	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs8051314	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8055288	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8064146	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9921359	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9938148	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1061359	chr16:81349826-81471867	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv542992	chr16:81349826-81471867	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9922086	GAN	cis	parietal	SCAN
rs9922086	MYOT	trans	parietal	SCAN
rs9922086	GAN	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81379400-81410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:81380600-81396200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:81381200-81396000	Weak transcription	Right Ventricle	heart
4	chr16:81382400-81396200	Weak transcription	Pancreas	Pancrea
5	chr16:81382400-81418400	Weak transcription	Small Intestine	intestine
6	chr16:81382600-81396000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr16:81382600-81398600	Weak transcription	Fetal Thymus	thymus
8	chr16:81383000-81395200	Weak transcription	Fetal Brain Female	brain
9	chr16:81383000-81395800	Weak transcription	Brain Germinal Matrix	brain
10	chr16:81383000-81396200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr16:81383200-81396000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr16:81383400-81395800	Weak transcription	Colonic Mucosa	Colon
13	chr16:81383400-81398000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr16:81383600-81395400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:81383600-81398600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr16:81383800-81396200	Weak transcription	Spleen	Spleen
17	chr16:81384000-81395600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr16:81384000-81398400	Weak transcription	NH-A	brain
19	chr16:81384000-81404800	Weak transcription	Stomach Mucosa	stomach
20	chr16:81384000-81410600	Weak transcription	Fetal Kidney	kidney
21	chr16:81384200-81434600	Weak transcription	NHLF	lung
22	chr16:81384200-81437400	Weak transcription	Fetal Brain Male	brain
23	chr16:81385000-81406200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:81385400-81410800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr16:81385600-81418200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:81385800-81396000	Weak transcription	Brain Hippocampus Middle	brain
27	chr16:81385800-81399800	Strong transcription	Primary T cells from cord blood	blood
28	chr16:81386200-81396000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr16:81386400-81395000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr16:81386400-81424200	Weak transcription	Psoas Muscle	Psoas
31	chr16:81387000-81428600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr16:81387200-81393800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr16:81387200-81407000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr16:81387200-81408200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr16:81387400-81393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:81387400-81400200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr16:81387600-81393800	Strong transcription	HepG2	liver
38	chr16:81387600-81405800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr16:81387600-81415200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:81387800-81393800	Strong transcription	Adipose Nuclei	Adipose
41	chr16:81388000-81394000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr16:81388000-81397200	Weak transcription	Brain Anterior Caudate	brain
43	chr16:81388000-81400200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr16:81388000-81407600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:81388200-81394000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr16:81388600-81396000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr16:81388800-81410200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr16:81389000-81395200	Weak transcription	Fetal Intestine Small	intestine
49	chr16:81389000-81395800	Weak transcription	Aorta	Aorta
50	chr16:81390000-81396200	Weak transcription	Brain Cingulate Gyrus	brain

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