Variant report

Variant	rs4974083
Chromosome Location	chr3:49000626-49000627
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	chr3:48992949..48995743-chr3:48999208..49001793,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11130181	0.81[EUR][1000 genomes]
rs11707968	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12715430	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13099075	0.87[EUR][1000 genomes]
rs3087866	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4292260	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs4955411	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs4955416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4955426	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs4974081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4974088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62259536	0.91[EUR][1000 genomes]
rs6414614	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6446200	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6446204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446247	0.85[EUR][1000 genomes]
rs6766238	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6772452	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs6787808	1.00[CEU][hapmap]
rs6798112	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7100	0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7372883	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7373072	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7429596	0.81[EUR][1000 genomes]
rs7434187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621347	0.81[EUR][1000 genomes]
rs7639370	0.83[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9311431	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9810318	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9864243	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9865051	0.95[CEU][hapmap];0.93[TSI][hapmap]
rs9873227	0.81[EUR][1000 genomes]
rs9879978	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs4974083	WDR6	cis	Nerve Tibial	GTEx
rs4974083	AMT	cis	parietal	SCAN
rs4974083	AMT	cis	cerebellum	SCAN
rs4974083	AMT	cis	Esophagus Mucosa	GTEx
rs4974083	NICN1-AS1	cis	Thyroid	GTEx
rs4974083	LZTFL1	cis	cerebellum	SCAN
rs4974083	NICN1	cis	parietal	SCAN
rs4974083	WDR6	cis	Muscle Skeletal	GTEx
rs4974083	QRICH1	cis	cerebellum	SCAN
rs4974083	AMT	cis	lung	GTEx
rs4974083	AMT	cis	lymphoblastoid	seeQTL
rs4974083	ZNF589	cis	parietal	SCAN
rs4974083	WDR6	cis	cerebellum	SCAN
rs4974083	AMT	cis	Artery Aorta	GTEx
rs4974083	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4974083	AMT	cis	Nerve Tibial	GTEx
rs4974083	NICN1	cis	Thyroid	GTEx
rs4974083	AMT	cis	Artery Tibial	GTEx
rs4974083	AMT	cis	Whole Blood	GTEx
rs4974083	GPX1	cis	parietal	SCAN
rs4974083	P4HTM	cis	parietal	SCAN
rs4974083	DALRD3	cis	parietal	SCAN
rs4974083	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4974083	NICN1	cis	cerebellum	SCAN
rs4974083	DALRD3	cis	cerebellum	SCAN
rs4974083	WDR6	cis	parietal	SCAN
rs4974083	NCKIPSD	cis	parietal	SCAN
rs4974083	IQCF1	cis	cerebellum	SCAN
rs4974083	PHF7	cis	parietal	SCAN
rs4974083	TLR9	cis	parietal	SCAN
rs4974083	AMT	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48957400-49003800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48965200-49004200	Weak transcription	Colonic Mucosa	Colon
3	chr3:48965800-49004000	Weak transcription	Fetal Brain Male	brain
4	chr3:48966000-49008000	Weak transcription	Fetal Kidney	kidney
5	chr3:48970400-49004400	Weak transcription	Pancreas	Pancrea
6	chr3:48970800-49002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:48979000-49007600	Weak transcription	Stomach Mucosa	stomach
8	chr3:48981400-49002200	Weak transcription	A549	lung
9	chr3:48982800-49002800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:48986600-49004400	Weak transcription	NHLF	lung
11	chr3:48987000-49004000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:48987000-49004200	Weak transcription	Aorta	Aorta
13	chr3:48987200-49002200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:48987200-49002200	Weak transcription	HMEC	breast
15	chr3:48988000-49011600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:48989800-49003000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:48989800-49023600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:48990000-49024600	Strong transcription	Fetal Thymus	thymus
19	chr3:48990200-49004000	Weak transcription	Small Intestine	intestine
20	chr3:48990200-49004400	Weak transcription	Brain Angular Gyrus	brain
21	chr3:48990200-49010000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:48992200-49003600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:48994200-49023800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:48994400-49023600	Strong transcription	Dnd41	blood
25	chr3:48994800-49010000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:48994800-49022000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:48995800-49002200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:48995800-49003000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:48995800-49003800	Weak transcription	Gastric	stomach
30	chr3:48995800-49004200	Weak transcription	Ovary	ovary
31	chr3:48995800-49004400	Weak transcription	Brain Substantia Nigra	brain
32	chr3:48995800-49004400	Weak transcription	K562	blood
33	chr3:48995800-49008000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:48996000-49003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:48996400-49002000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:48996400-49002200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:48997200-49001200	Strong transcription	NHEK	skin
38	chr3:48997400-49001000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:48997800-49003800	Weak transcription	Brain Anterior Caudate	brain
40	chr3:48997800-49009400	Weak transcription	Psoas Muscle	Psoas
41	chr3:48998800-49001200	Strong transcription	Liver	Liver
42	chr3:48998800-49001200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:48998800-49004000	Weak transcription	NHDF-Ad	bronchial
44	chr3:48998800-49023400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:48999000-49000800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:48999000-49000800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr3:48999000-49000800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:48999000-49001000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:48999000-49001200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:48999000-49001200	Strong transcription	HSMM	muscle

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