Variant report

Variant	rs3817599
Chromosome Location	chr3:121659197-121659198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121466815..121468443-chr3:121658267..121660629,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10934568	0.90[JPT][hapmap]
rs11916150	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12489511	0.84[GIH][hapmap]
rs12490565	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs12695420	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068522	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474327	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1589700	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2091665	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2141614	0.90[JPT][hapmap]
rs2332056	0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs2689276	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2700424	0.89[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34227248	0.82[AMR][1000 genomes]
rs4419417	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770115	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6770719	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs6780559	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181839	0.82[AMR][1000 genomes]
rs7626740	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628167	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638094	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7647751	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289185	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs953730	0.92[ASW][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9815649	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9828757	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9829181	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843053	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS 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
2	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv877384	chr3:121601577-121659774	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3817599	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs3817599	MUC13	cis	cerebellum	SCAN
rs3817599	CCDC14	cis	cerebellum	SCAN
rs3817599	ADPRH	cis	parietal	SCAN
rs3817599	MYLK	cis	cerebellum	SCAN
rs3817599	SLC15A2	cis	parietal	SCAN
rs3817599	SLC15A2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
2	chr3:121616200-121659400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:121625000-121661200	Weak transcription	Thymus	Thymus
4	chr3:121627400-121659200	Weak transcription	Lung	lung
5	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
6	chr3:121627600-121659200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:121628200-121659200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:121633200-121661200	Weak transcription	Liver	Liver
10	chr3:121633800-121661200	Weak transcription	Right Ventricle	heart
11	chr3:121634000-121660400	Weak transcription	Fetal Kidney	kidney
12	chr3:121634800-121667000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:121635200-121666800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:121638400-121664800	Weak transcription	Spleen	Spleen
16	chr3:121638600-121661000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:121638800-121661000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:121640800-121659400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:121642400-121661600	Weak transcription	Fetal Thymus	thymus
20	chr3:121643400-121659200	Weak transcription	Fetal Lung	lung
21	chr3:121644000-121661200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:121646600-121661800	Weak transcription	Ovary	ovary
23	chr3:121646800-121666200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:121647200-121659400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:121647200-121660600	Weak transcription	Small Intestine	intestine
26	chr3:121647400-121659200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:121648800-121659800	Weak transcription	Left Ventricle	heart
28	chr3:121650000-121659200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:121650600-121665800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:121650600-121675600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:121651200-121664000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:121652800-121659600	Weak transcription	Placenta	Placenta
33	chr3:121656400-121667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:121656800-121661000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:121656800-121675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:121657000-121664600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:121657200-121662600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:121657400-121661000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:121657600-121660200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:121657600-121660200	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:121657600-121661200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:121657600-121662600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:121657600-121663200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:121657600-121663600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:121657600-121666000	Strong transcription	Primary B cells from cord blood	blood
46	chr3:121657800-121659600	Strong transcription	GM12878-XiMat	blood
47	chr3:121657800-121660400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:121657800-121665200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:121658000-121660200	Strong transcription	Primary T cells from cord blood	blood
50	chr3:121658000-121660200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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