Variant report

Variant	rs1564116
Chromosome Location	chr16:81388702-81388703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81386617..81388952-chr16:81390727..81393238,2	K562	blood:
2	chr16:81381387..81385191-chr16:81386059..81389530,5	K562	blood:
3	chr16:81388209..81391799-chr16:81392393..81395438,3	MCF-7	breast:
4	chr16:81348969..81350661-chr16:81387216..81389989,2	MCF-7	breast:
5	chr16:81384234..81386036-chr16:81388157..81390233,2	MCF-7	breast:
6	chr16:81387085..81388738-chr8:143273482..143275367,2	MCF-7	breast:
7	chr16:81381387..81384964-chr16:81385741..81388867,5	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12103052	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12448813	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12920172	0.85[YRI][hapmap]
rs12921222	0.92[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12925218	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12927652	1.00[CEU][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12929924	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12933277	0.92[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12934500	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16955063	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1820260	0.92[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35151165	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888145	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4889309	0.92[CEU][hapmap]
rs6564872	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs7194094	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7199407	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7199797	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7203482	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7203835	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs729181	1.00[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs8051314	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8055288	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8064146	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9921359	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9922086	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]
rs9938148	1.00[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[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	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
6	esv1792674	chr16:81375316-81391868	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1564116	GAN	cis	cerebellum	SCAN
rs1564116	MYOT	trans	parietal	SCAN
rs1564116	GAN	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81353400-81390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:81354200-81391600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr16:81379400-81410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:81380600-81396200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:81381000-81392600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr16:81381200-81390200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr16:81381200-81390400	Weak transcription	Brain Substantia Nigra	brain
8	chr16:81381200-81391000	Weak transcription	Osteobl	bone
9	chr16:81381200-81396000	Weak transcription	Right Ventricle	heart
10	chr16:81382200-81390200	Weak transcription	NHEK	skin
11	chr16:81382200-81391400	Weak transcription	Fetal Heart	heart
12	chr16:81382400-81390400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr16:81382400-81390400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:81382400-81391400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr16:81382400-81396200	Weak transcription	Pancreas	Pancrea
16	chr16:81382400-81418400	Weak transcription	Small Intestine	intestine
17	chr16:81382600-81390200	Weak transcription	A549	lung
18	chr16:81382600-81391400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:81382600-81391400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr16:81382600-81391400	Weak transcription	Brain Angular Gyrus	brain
21	chr16:81382600-81396000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr16:81382600-81398600	Weak transcription	Fetal Thymus	thymus
23	chr16:81382800-81390400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr16:81382800-81391400	Weak transcription	Thymus	Thymus
25	chr16:81383000-81391400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr16:81383000-81391400	Weak transcription	HSMM	muscle
27	chr16:81383000-81391400	Weak transcription	HUVEC	blood vessel
28	chr16:81383000-81395200	Weak transcription	Fetal Brain Female	brain
29	chr16:81383000-81395800	Weak transcription	Brain Germinal Matrix	brain
30	chr16:81383000-81396200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:81383200-81390200	Weak transcription	Gastric	stomach
32	chr16:81383200-81391400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr16:81383200-81396000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr16:81383400-81395800	Weak transcription	Colonic Mucosa	Colon
35	chr16:81383400-81398000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr16:81383600-81395400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr16:81383600-81398600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr16:81383800-81390000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr16:81383800-81390200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr16:81383800-81391400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:81383800-81396200	Weak transcription	Spleen	Spleen
42	chr16:81384000-81390400	Weak transcription	NHDF-Ad	bronchial
43	chr16:81384000-81395600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr16:81384000-81398400	Weak transcription	NH-A	brain
45	chr16:81384000-81404800	Weak transcription	Stomach Mucosa	stomach
46	chr16:81384000-81410600	Weak transcription	Fetal Kidney	kidney
47	chr16:81384200-81388800	Weak transcription	Dnd41	blood
48	chr16:81384200-81434600	Weak transcription	NHLF	lung
49	chr16:81384200-81437400	Weak transcription	Fetal Brain Male	brain
50	chr16:81384400-81390400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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