Variant report

Variant	rs586946
Chromosome Location	chr3:138299292-138299293
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10804658	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1082034	0.84[EUR][1000 genomes]
rs1082037	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1088055	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935284	0.81[AFR][1000 genomes]
rs10935287	0.88[EUR][1000 genomes]
rs11717771	0.88[EUR][1000 genomes]
rs12487652	0.88[EUR][1000 genomes]
rs12487694	0.87[EUR][1000 genomes]
rs12490633	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs12497070	0.88[EUR][1000 genomes]
rs12636910	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs13101081	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1379257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1479930	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1600511	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1672927	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1672928	0.81[CEU][hapmap]
rs1672932	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1672938	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1672939	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1672963	0.86[EUR][1000 genomes]
rs1673593	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1673594	0.86[EUR][1000 genomes]
rs1673607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1673608	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1673612	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1673622	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs1673624	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1679167	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1679168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1679175	0.86[AMR][1000 genomes]
rs1720836	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs2124868	0.81[EUR][1000 genomes]
rs2347469	1.00[JPT][hapmap]
rs2348146	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2607790	0.87[EUR][1000 genomes]
rs2607795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs361073	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361074	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361075	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361076	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs361077	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3884240	0.89[CEU][hapmap]
rs3884241	0.90[CEU][hapmap]
rs4432674	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4678264	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4678265	0.81[AFR][1000 genomes]
rs4678420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs484698	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4894389	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs497334	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs503922	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs529615	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs537210	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs542010	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs550507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs559313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564800	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs579750	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs582386	0.81[EUR][1000 genomes]
rs587005	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs587331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60513493	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs609497	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs609797	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs611134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs612471	0.80[EUR][1000 genomes]
rs61699523	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs618792	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs620035	0.84[EUR][1000 genomes]
rs629884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs634374	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs642258	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6439809	0.90[CEU][hapmap];0.80[AMR][1000 genomes]
rs6439810	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs664928	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6771237	0.81[EUR][1000 genomes]
rs6798058	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs680070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7625326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7626226	0.96[CEU][hapmap]
rs7627685	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7634745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7643973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645920	0.90[CEU][hapmap]
rs7653815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs773444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs773445	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs773448	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs773449	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs773450	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs773452	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs773456	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs774003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs774005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs774008	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs774015	0.82[CEU][hapmap]
rs808925	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs811322	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs811793	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs814022	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs936316	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs9681127	0.85[EUR][1000 genomes]
rs9811052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9817419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9827256	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9848718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9853998	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9878436	0.89[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv877538	chr3:138218709-138311201	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
11	esv3448925	chr3:138277303-138312046	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs586946	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs586946	CEP70	cis	Muscle Skeletal	GTEx
rs586946	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138269000-138306800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:138279600-138300400	Weak transcription	Colonic Mucosa	Colon
3	chr3:138280000-138311200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:138285200-138307200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:138288200-138299400	Weak transcription	HSMM	muscle
6	chr3:138288200-138312400	Weak transcription	Ovary	ovary
7	chr3:138289000-138310600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:138290200-138312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:138291200-138310000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:138292200-138304400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:138293200-138300000	Weak transcription	Esophagus	oesophagus
12	chr3:138293200-138304400	Weak transcription	Fetal Lung	lung
13	chr3:138293200-138305200	Weak transcription	Liver	Liver
14	chr3:138293200-138310600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:138293200-138311800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:138293200-138312600	Weak transcription	Aorta	Aorta
17	chr3:138293400-138307600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:138293400-138312000	Weak transcription	Adipose Nuclei	Adipose
19	chr3:138293400-138312600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:138293800-138310000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:138293800-138311400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:138296600-138306400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:138297200-138299400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr3:138297200-138304800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:138297200-138311000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:138297400-138299600	Enhancers	Fetal Thymus	thymus
27	chr3:138297400-138303400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:138297400-138311000	Weak transcription	NHDF-Ad	bronchial
29	chr3:138297400-138311600	Weak transcription	Osteobl	bone
30	chr3:138297600-138312000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:138297800-138299400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:138297800-138299400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:138297800-138299400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:138297800-138299400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:138297800-138299600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:138298000-138299400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:138298000-138302200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:138298000-138312400	Weak transcription	Primary T cells from cord blood	blood
39	chr3:138298200-138302000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:138298200-138312200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:138298400-138312400	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:138298400-138312400	Weak transcription	Psoas Muscle	Psoas
43	chr3:138298600-138302200	Weak transcription	Brain Substantia Nigra	brain
44	chr3:138298600-138307000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:138298600-138307200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:138298600-138311400	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:138298600-138311800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:138298800-138310800	Weak transcription	HepG2	liver
49	chr3:138298800-138311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:138299000-138307400	Weak transcription	Fetal Heart	heart

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