Variant report

Variant	rs9828205
Chromosome Location	chr3:160806859-160806860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160796262..160798451-chr3:160804894..160807595,2	K562	blood:
2	chr3:160786158..160788283-chr3:160805883..160807587,2	K562	blood:
3	chr3:160805899..160808057-chr3:161089198..161091341,2	MCF-7	breast:
4	chr3:160792122..160793985-chr3:160805290..160807402,2	K562	blood:
5	chr3:160806758..160810254-chr3:160813169..160817667,5	MCF-7	breast:
6	chr3:160803828..160805818-chr3:160806388..160808521,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045448	0.81[EUR][1000 genomes]
rs12488037	0.93[EUR][1000 genomes]
rs12494844	0.93[EUR][1000 genomes]
rs13314089	0.89[ASN][1000 genomes]
rs13318781	0.93[EUR][1000 genomes]
rs13319969	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13320863	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599380	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1599384	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1599391	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1947685	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1947686	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1970834	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2231252	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28623696	0.82[AMR][1000 genomes]
rs35152606	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35440670	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35446590	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35599916	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36105583	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4270539	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4443220	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4465984	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4490410	0.93[EUR][1000 genomes]
rs62278031	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62278055	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441353	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6795977	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs68159406	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs731363	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73160351	0.89[EUR][1000 genomes]
rs7630896	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7634115	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9290067	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9290068	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9810737	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9817747	0.92[ASN][1000 genomes]
rs9818516	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9824308	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824501	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9825118	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9829882	0.81[EUR][1000 genomes]
rs9830139	0.81[EUR][1000 genomes]
rs9834751	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9836074	0.98[EUR][1000 genomes]
rs9840389	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9842281	0.93[EUR][1000 genomes]
rs9851292	0.85[ASN][1000 genomes]
rs9858399	0.93[EUR][1000 genomes]
rs9861850	0.84[EUR][1000 genomes]
rs9862258	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9878365	0.93[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9828205	DNMT1	trans	lymphoblastoid	RTeQTL
rs9828205	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
2	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
3	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:160788600-160807600	Weak transcription	Pancreas	Pancrea
6	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
7	chr3:160796000-160817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:160796200-160821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:160797600-160817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:160798600-160821800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:160799800-160821800	Weak transcription	NHLF	lung
13	chr3:160799800-160822000	Weak transcription	HMEC	breast
14	chr3:160800200-160808000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:160800200-160818200	Weak transcription	Fetal Intestine Small	intestine
16	chr3:160800200-160820000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:160800400-160813400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:160800400-160817200	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:160800400-160818800	Weak transcription	Gastric	stomach
20	chr3:160800400-160822200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
22	chr3:160800600-160807800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:160801000-160821800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:160801200-160822000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:160801600-160816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:160801600-160818800	Weak transcription	Placenta	Placenta
27	chr3:160801600-160821800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:160802200-160808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:160802600-160821400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:160802600-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:160802800-160822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:160803000-160807600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:160803200-160807200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr3:160803200-160808000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:160803400-160807000	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:160803400-160807200	Strong transcription	Fetal Lung	lung
38	chr3:160803400-160807800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:160803400-160819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:160803400-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:160803800-160808000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:160803800-160822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:160804400-160807000	Weak transcription	Liver	Liver
44	chr3:160804400-160811800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:160804400-160816600	Weak transcription	Fetal Brain Female	brain
46	chr3:160804400-160818200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:160804400-160822000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:160804400-160822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:160804600-160812800	Weak transcription	Aorta	Aorta
50	chr3:160804600-160813000	Weak transcription	Fetal Intestine Large	intestine

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