Variant report

Variant	rs9862483
Chromosome Location	chr3:49195441-49195442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
2	chr3:49058901..49061123-chr3:49194988..49197137,2	MCF-7	breast:
3	chr3:49186129..49188864-chr3:49193621..49196064,2	MCF-7	breast:
4	chr3:49140848..49143633-chr3:49193984..49195693,2	MCF-7	breast:
5	chr3:49188624..49190754-chr3:49194222..49196176,2	K562	blood:
6	chr3:49195403..49197616-chr3:49208526..49210728,2	K562	blood:
7	chr3:49062671..49068005-chr3:49193889..49197259,7	MCF-7	breast:
8	chr3:49189882..49192619-chr3:49194424..49197107,3	MCF-7	breast:
9	chr3:49173300..49174828-chr3:49194938..49196550,2	K562	blood:
10	chr3:49042896..49045458-chr3:49193854..49196447,2	MCF-7	breast:
11	chr3:49193599..49196325-chr3:49216577..49219891,3	MCF-7	breast:
12	chr3:49063218..49064787-chr3:49194853..49197640,2	K562	blood:
13	chr3:49141127..49143388-chr3:49194740..49196446,2	MCF-7	breast:
14	chr3:49070051..49071657-chr3:49195116..49197322,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272434	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000178252	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10049462	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10154895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865954	0.89[ASN][1000 genomes]
rs11130182	0.88[ASN][1000 genomes]
rs11130184	0.87[ASN][1000 genomes]
rs11552724	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11706052	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706189	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710247	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712006	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11713297	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715581	0.92[ASN][1000 genomes]
rs11716334	0.87[ASN][1000 genomes]
rs11718982	0.88[EUR][1000 genomes]
rs11719220	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719457	0.81[EUR][1000 genomes]
rs11720460	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12487580	0.90[ASN][1000 genomes]
rs12490393	0.92[ASN][1000 genomes]
rs12493001	1.00[ASN][1000 genomes]
rs12629759	0.87[ASN][1000 genomes]
rs12636030	1.00[ASN][1000 genomes]
rs12637576	0.87[ASN][1000 genomes]
rs12715434	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13064784	0.85[ASN][1000 genomes]
rs13068038	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072554	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077498	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13080725	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086240	0.81[EUR][1000 genomes]
rs13087930	0.81[EUR][1000 genomes]
rs13090839	0.81[EUR][1000 genomes]
rs13096406	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28690891	0.81[AFR][1000 genomes]
rs3212	0.85[ASN][1000 genomes]
rs34326553	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34343820	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34504524	0.84[EUR][1000 genomes]
rs34509487	0.81[EUR][1000 genomes]
rs34566463	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34580506	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34784192	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34889065	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35060561	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35102816	0.84[EUR][1000 genomes]
rs35108630	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35185152	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35283189	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35673421	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3923475	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279134	0.85[ASN][1000 genomes]
rs4308307	0.92[ASN][1000 genomes]
rs4364202	0.83[ASN][1000 genomes]
rs4499638	0.97[ASN][1000 genomes]
rs4513485	0.85[ASN][1000 genomes]
rs4521268	0.85[ASN][1000 genomes]
rs4536858	0.97[ASN][1000 genomes]
rs4955410	0.95[ASN][1000 genomes]
rs4955418	0.97[ASN][1000 genomes]
rs4955419	0.92[ASN][1000 genomes]
rs4955420	0.92[ASN][1000 genomes]
rs5030795	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55713230	0.97[ASN][1000 genomes]
rs55921200	0.83[EUR][1000 genomes]
rs56306491	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56318350	0.81[EUR][1000 genomes]
rs61583136	0.95[ASN][1000 genomes]
rs62262517	0.83[ASN][1000 genomes]
rs66991555	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67286839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6770112	0.95[ASN][1000 genomes]
rs6779394	0.89[ASN][1000 genomes]
rs67831908	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6784111	1.00[ASN][1000 genomes]
rs6790914	0.97[ASN][1000 genomes]
rs6794924	0.87[ASN][1000 genomes]
rs6795025	0.81[ASN][1000 genomes]
rs71324939	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7615235	0.82[ASN][1000 genomes]
rs7626445	0.85[ASN][1000 genomes]
rs9311439	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814987	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826525	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9828310	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9835439	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837237	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9837625	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840050	0.85[ASN][1000 genomes]
rs9847839	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850917	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9855123	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880309	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9990153	0.90[AMR][1000 genomes];0.95[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	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9862483	WDR6	cis	Artery Tibial	GTEx
rs9862483	WDR6	cis	Adipose Subcutaneous	GTEx
rs9862483	WDR6	cis	Esophagus Mucosa	GTEx
rs9862483	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs9862483	WDR6	cis	Whole Blood	GTEx
rs9862483	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49186200-49198800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:49186800-49198800	Weak transcription	Pancreas	Pancrea
4	chr3:49191000-49198800	Weak transcription	Ovary	ovary
5	chr3:49191000-49199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49191400-49198800	Weak transcription	Gastric	stomach
7	chr3:49191400-49199000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:49191600-49200200	Weak transcription	Esophagus	oesophagus
9	chr3:49192000-49198000	Weak transcription	Thymus	Thymus
10	chr3:49192200-49198600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:49194200-49196000	Weak transcription	Fetal Stomach	stomach
12	chr3:49194400-49198200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:49194400-49199000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:49194600-49198200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:49194600-49198800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:49194800-49198200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:49195000-49195800	Enhancers	Fetal Intestine Large	intestine
18	chr3:49195000-49196400	Enhancers	HepG2	liver
19	chr3:49195000-49198200	Weak transcription	Fetal Brain Female	brain
20	chr3:49195000-49198200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:49195000-49199600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:49195200-49195800	Enhancers	Brain Substantia Nigra	brain
23	chr3:49195200-49195800	Enhancers	Fetal Intestine Small	intestine
24	chr3:49195200-49197000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr3:49195200-49199400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:49195200-49200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:49195200-49202400	Weak transcription	Fetal Kidney	kidney
28	chr3:49195400-49195600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:49195400-49195600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:49195400-49195600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:49195400-49195600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:49195400-49195600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:49195400-49195600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:49195400-49195600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:49195400-49195600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:49195400-49195600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:49195400-49195600	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:49195400-49195600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:49195400-49195600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:49195400-49195600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:49195400-49195600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:49195400-49195600	Enhancers	Fetal Muscle Leg	muscle
43	chr3:49195400-49195600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr3:49195400-49195800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:49195400-49196000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:49195400-49196400	Weak transcription	Hela-S3	cervix
47	chr3:49195400-49198800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:49195400-49200400	Weak transcription	Brain Angular Gyrus	brain

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