Variant report

Variant	rs13079082
Chromosome Location	chr3:49574808-49574809
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49573308..49575381-chr3:49575652..49577687,3	K562	blood:
2	chr3:49573379..49575748-chr3:49707460..49709611,2	MCF-7	breast:
3	chr3:49572260..49575094-chr3:49709168..49713049,4	K562	blood:
4	chr3:49567781..49571690-chr3:49573086..49576036,4	K562	blood:
5	chr3:49574299..49577116-chr3:49756241..49758538,2	K562	blood:
6	chr3:49573308..49575381-chr3:49575652..49577242,2	K562	blood:
7	chr3:49554866..49557118-chr3:49574115..49576827,2	K562	blood:

Variant related genes	Relation type
ENSG00000164062	Chromatin interaction
ENSG00000176020	Chromatin interaction
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10212296	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1050088	0.94[ASN][1000 genomes]
rs1050450	0.82[AMR][1000 genomes]
rs10640	0.83[AMR][1000 genomes]
rs10865955	0.82[ASN][1000 genomes]
rs11130199	0.94[ASN][1000 genomes]
rs11130202	0.94[ASN][1000 genomes]
rs11130203	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130206	0.84[ASN][1000 genomes]
rs11706370	0.83[AMR][1000 genomes]
rs11708955	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11711485	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11712569	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713474	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715915	0.83[AMR][1000 genomes]
rs11716974	0.83[AMR][1000 genomes]
rs11719996	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720264	0.94[ASN][1000 genomes]
rs11720458	0.86[ASN][1000 genomes]
rs11720597	0.91[EUR][1000 genomes]
rs11922013	0.88[AMR][1000 genomes]
rs11926781	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12330269	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488065	0.88[ASN][1000 genomes]
rs12489092	0.94[ASN][1000 genomes]
rs13062429	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13064576	0.89[EUR][1000 genomes]
rs13079643	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13087851	0.80[AMR][1000 genomes]
rs13090388	0.82[AMR][1000 genomes]
rs1568661	0.94[ASN][1000 genomes]
rs17080528	0.82[AMR][1000 genomes]
rs1800668	0.80[AMR][1000 genomes]
rs1801143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987628	0.80[AMR][1000 genomes]
rs2312461	0.94[ASN][1000 genomes]
rs34196454	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34293138	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34363169	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34427167	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34588335	0.82[AMR][1000 genomes]
rs35115732	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35169793	0.82[AMR][1000 genomes]
rs35261698	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35701831	0.94[ASN][1000 genomes]
rs35999162	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811697	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811699	0.82[AMR][1000 genomes]
rs3870337	0.94[ASN][1000 genomes]
rs3870338	0.94[ASN][1000 genomes]
rs3877784	0.94[ASN][1000 genomes]
rs3924462	0.94[ASN][1000 genomes]
rs3926569	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241406	0.86[ASN][1000 genomes]
rs4625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855836	0.94[ASN][1000 genomes]
rs4855855	0.85[ASN][1000 genomes]
rs4855859	0.94[ASN][1000 genomes]
rs4855861	0.94[ASN][1000 genomes]
rs4855864	0.94[ASN][1000 genomes]
rs4855866	0.80[ASN][1000 genomes]
rs56116382	0.87[ASN][1000 genomes]
rs62261185	0.81[ASN][1000 genomes]
rs6446264	0.80[AMR][1000 genomes]
rs6446272	0.88[AMR][1000 genomes]
rs6446277	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67216675	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67485053	0.80[AMR][1000 genomes]
rs6766131	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766581	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779524	0.85[AMR][1000 genomes]
rs6793308	0.82[AMR][1000 genomes]
rs6797664	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809216	0.82[AMR][1000 genomes]
rs6997	0.85[AMR][1000 genomes]
rs71324962	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71615484	0.96[ASN][1000 genomes]
rs7371895	0.82[ASN][1000 genomes]
rs7622302	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623659	0.82[AMR][1000 genomes]
rs7630869	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633271	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637999	0.94[ASN][1000 genomes]
rs7643845	0.94[ASN][1000 genomes]
rs7646366	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7648841	0.80[AMR][1000 genomes]
rs885592	0.82[ASN][1000 genomes]
rs9814873	0.83[AMR][1000 genomes]
rs9818590	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821311	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9827021	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837027	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9841110	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850072	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853683	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858280	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858418	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9859556	0.86[AMR][1000 genomes]
rs9871380	0.85[AMR][1000 genomes]
rs9875617	0.92[EUR][1000 genomes]
rs9878943	0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13079082	FAM212A	cis	Muscle Skeletal	GTEx
rs13079082	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs13079082	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49546200-49577000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:49548400-49577400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:49568200-49577000	Weak transcription	HMEC	breast
4	chr3:49568800-49576800	Weak transcription	Fetal Heart	heart
5	chr3:49569000-49576800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:49569800-49577000	Weak transcription	Fetal Lung	lung
7	chr3:49569800-49577400	Weak transcription	Fetal Kidney	kidney
8	chr3:49570000-49576800	Weak transcription	K562	blood
9	chr3:49570200-49576800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:49570200-49577200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:49570200-49577400	Weak transcription	Small Intestine	intestine
12	chr3:49570400-49577400	Weak transcription	GM12878-XiMat	blood
13	chr3:49570600-49577000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:49570600-49577000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:49570600-49577400	Weak transcription	HUVEC	blood vessel
16	chr3:49570800-49577000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:49570800-49577000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:49570800-49577000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:49570800-49577000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:49570800-49577000	Weak transcription	NHEK	skin
21	chr3:49570800-49577200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:49570800-49577400	Weak transcription	Aorta	Aorta
23	chr3:49571000-49576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:49571000-49576800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:49571000-49577000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:49571000-49577000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:49571000-49577400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:49571200-49576800	Weak transcription	Dnd41	blood
29	chr3:49571200-49577000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49571200-49577000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:49571200-49577400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:49571200-49577400	Weak transcription	Primary B cells from cord blood	blood
33	chr3:49571200-49577400	Weak transcription	A549	lung
34	chr3:49571400-49575000	Enhancers	Liver	Liver
35	chr3:49571400-49576800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:49571400-49576800	Weak transcription	Fetal Thymus	thymus
37	chr3:49571400-49577000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:49571400-49577000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:49571400-49577200	Weak transcription	Primary T cells from cord blood	blood
40	chr3:49571400-49577400	Weak transcription	Lung	lung
41	chr3:49571600-49575200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:49571600-49577000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:49571600-49577000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:49571600-49577000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:49571600-49577200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:49571600-49577400	Weak transcription	Esophagus	oesophagus
47	chr3:49571600-49577400	Weak transcription	Left Ventricle	heart
48	chr3:49571800-49576800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:49571800-49576800	Weak transcription	Hela-S3	cervix
50	chr3:49571800-49577000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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