Variant report

Variant	rs3749563
Chromosome Location	chr4:152596508-152596509
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	chr4:152586811..152588784-chr4:152594944..152597793,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM160A1-2	chr4:152595635-152597712	ENSG00000251455.1

Variant related genes	Relation type
ENSG00000251603	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10007015	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10007167	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10019048	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023298	0.86[EUR][1000 genomes]
rs10028410	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10028961	0.86[EUR][1000 genomes]
rs10049728	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10049991	0.86[EUR][1000 genomes]
rs10776524	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105534	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1105535	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105536	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734799	0.81[EUR][1000 genomes]
rs12331037	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12502055	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137669	0.82[EUR][1000 genomes]
rs13138986	0.81[EUR][1000 genomes]
rs13146981	0.81[EUR][1000 genomes]
rs13149588	0.96[CEU][hapmap]
rs1355413	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1366909	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1511170	0.84[EUR][1000 genomes]
rs17027798	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17360475	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1864300	0.85[EUR][1000 genomes]
rs1877187	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1896883	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007218	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2007445	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278304	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2303866	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2840130	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28637056	0.87[EUR][1000 genomes]
rs28710456	0.86[EUR][1000 genomes]
rs3749561	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3792691	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3919716	0.84[EUR][1000 genomes]
rs4383600	0.84[EUR][1000 genomes]
rs4571	1.00[CEU][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696104	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696109	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4696111	0.86[EUR][1000 genomes]
rs4696277	0.93[EUR][1000 genomes]
rs4696283	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4696284	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696285	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696291	0.90[EUR][1000 genomes]
rs4696293	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4696294	0.81[EUR][1000 genomes]
rs55668815	0.86[EUR][1000 genomes]
rs6535809	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535811	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535812	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535813	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535814	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535815	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535817	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6535818	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6535819	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6535821	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6810860	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817058	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817586	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6818667	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823002	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823194	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823421	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823423	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823462	0.83[EUR][1000 genomes]
rs6825241	0.80[EUR][1000 genomes]
rs6832562	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833368	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834095	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838966	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839074	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840360	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840678	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841204	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841783	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845944	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846114	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849050	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7439465	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749982	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751012	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751014	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7663045	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7667197	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7669977	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7671651	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684350	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7695162	0.92[EUR][1000 genomes]
rs907237	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9307887	0.83[EUR][1000 genomes]
rs9995704	0.85[EUR][1000 genomes]
rs9998462	0.88[EUR][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	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1026511	chr4:152593382-152611915	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3749563	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:152579200-152597400	Weak transcription	Liver	Liver
5	chr4:152580800-152596800	Weak transcription	Primary T cells from cord blood	blood
6	chr4:152581200-152602800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:152581200-152608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:152585800-152600400	Weak transcription	Gastric	stomach
10	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:152586000-152596600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:152589200-152608800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:152589200-152619200	Weak transcription	Dnd41	blood
15	chr4:152590400-152601600	Weak transcription	Primary B cells from cord blood	blood
16	chr4:152590600-152597600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:152590600-152609000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:152591200-152597400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:152591200-152608600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:152592000-152598200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:152592200-152608000	Weak transcription	Thymus	Thymus
23	chr4:152592400-152597800	Enhancers	Left Ventricle	heart
24	chr4:152592600-152636400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:152593600-152608000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:152593600-152608800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:152594000-152600400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:152594200-152600400	Weak transcription	Fetal Thymus	thymus
29	chr4:152594800-152597200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:152595000-152596800	Enhancers	Lung	lung
31	chr4:152595200-152596800	Enhancers	Esophagus	oesophagus
32	chr4:152595200-152597200	Enhancers	Fetal Brain Male	brain
33	chr4:152595200-152598000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:152595200-152598800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:152595200-152611600	Weak transcription	K562	blood
36	chr4:152595400-152596800	Enhancers	Psoas Muscle	Psoas
37	chr4:152595600-152597200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:152595600-152602400	Weak transcription	HepG2	liver
39	chr4:152595600-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:152595800-152596600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr4:152595800-152596600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:152595800-152596600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:152595800-152596600	Active TSS	Colon Smooth Muscle	Colon
44	chr4:152595800-152597000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:152596000-152596600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr4:152596000-152596600	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr4:152596000-152596600	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr4:152596000-152597000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:152596000-152597000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:152596000-152598000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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