Variant report

Variant	rs3826154
Chromosome Location	chr16:69730555-69730556
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	chr16:69727892..69730821-chr16:69744925..69746570,2	K562	blood:
2	chr16:69727091..69731823-chr16:69734044..69738308,5	K562	blood:

Variant related genes	Relation type
ENSG00000260772	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10517	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10852459	0.85[CHB][hapmap]
rs1142105	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11862697	0.85[CEU][hapmap]
rs12019048	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs12102305	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12921017	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1318651	0.87[CEU][hapmap]
rs13329844	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13331055	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13331071	0.86[ASN][1000 genomes]
rs13331216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13335149	0.89[ASN][1000 genomes]
rs13335664	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13338560	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16958965	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16958997	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16959059	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16959266	0.87[CEU][hapmap]
rs2088747	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs2291960	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs2304526	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28392989	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28473508	0.82[ASN][1000 genomes]
rs2917665	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2917667	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2917669	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2917672	0.88[ASN][1000 genomes]
rs2917673	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2917674	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2917675	0.93[ASN][1000 genomes]
rs2917676	0.96[ASN][1000 genomes]
rs2917681	1.00[YRI][hapmap]
rs2917682	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs2917683	0.90[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs2937125	0.85[CHB][hapmap]
rs2937126	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs2965752	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2965753	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs2965757	0.90[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2965758	0.80[CHB][hapmap]
rs2965759	0.87[CEU][hapmap]
rs3785075	0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790087	0.87[CEU][hapmap]
rs3790088	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs3826153	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs3926183	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4247109	0.87[CEU][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap]
rs4442796	0.82[CHD][hapmap];0.86[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs4985527	0.87[CEU][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap]
rs4985547	0.85[CHB][hapmap]
rs61628167	0.85[ASN][1000 genomes]
rs6499246	0.90[ASN][1000 genomes]
rs6499249	0.84[CHD][hapmap];0.86[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs6499259	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs689452	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs689456	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7200420	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7359387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8057938	0.87[CEU][hapmap]
rs9888980	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs9888981	0.87[CEU][hapmap]
rs9888993	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9889219	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs9921652	0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs9922223	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs9924264	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9924271	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs9924953	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9925037	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9927809	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9932486	0.86[CEU][hapmap]
rs9934264	0.89[ASN][1000 genomes]
rs9934321	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9934681	1.00[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9936464	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9937018	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9938717	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs9940008	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 target site	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3826154	NOL3	cis	cerebellum	SCAN
rs3826154	CDH16	cis	cerebellum	SCAN
rs3826154	GFOD2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69701800-69739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr16:69704600-69737800	Strong transcription	Liver	Liver
3	chr16:69708800-69739600	Strong transcription	Placenta	Placenta
4	chr16:69709000-69739400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:69709800-69737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:69710000-69737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr16:69710800-69732000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr16:69715200-69737800	Strong transcription	HepG2	liver
10	chr16:69722400-69731800	Strong transcription	Osteobl	bone
11	chr16:69722400-69732600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr16:69722400-69737200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr16:69722600-69734600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:69722600-69738800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:69722800-69732200	Strong transcription	NH-A	brain
16	chr16:69722800-69739400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr16:69723400-69731800	Strong transcription	Hela-S3	cervix
18	chr16:69723400-69732000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:69723400-69732000	Strong transcription	HMEC	breast
20	chr16:69723600-69731800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr16:69723600-69733800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr16:69723600-69736200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr16:69723800-69732000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr16:69723800-69732000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr16:69723800-69733800	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr16:69723800-69739200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:69724000-69730600	Strong transcription	Brain Anterior Caudate	brain
28	chr16:69724000-69731800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:69724000-69732600	Strong transcription	Dnd41	blood
30	chr16:69724400-69731000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr16:69724600-69731800	Strong transcription	Primary B cells from cord blood	blood
32	chr16:69724600-69732200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr16:69724600-69732600	Strong transcription	Fetal Thymus	thymus
34	chr16:69724600-69733400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:69724600-69738400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr16:69724800-69731800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr16:69724800-69731800	Strong transcription	HUVEC	blood vessel
38	chr16:69724800-69731800	Strong transcription	NHEK	skin
39	chr16:69724800-69732000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr16:69724800-69732600	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr16:69724800-69736600	Strong transcription	Adipose Nuclei	Adipose
42	chr16:69725000-69730800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr16:69725000-69732200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr16:69725200-69733200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr16:69725400-69731600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr16:69725600-69731000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr16:69725600-69731800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr16:69725600-69731800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr16:69725600-69732000	Strong transcription	Fetal Muscle Leg	muscle
50	chr16:69725800-69730800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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