Variant report

Variant	rs9049
Chromosome Location	chr3:138213292-138213293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10935282	0.82[JPT][hapmap]
rs11709290	0.82[JPT][hapmap]
rs11916525	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12054428	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490633	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12630060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630144	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630351	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12631438	0.81[JPT][hapmap]
rs12632793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12635354	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635490	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12635904	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12636936	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637638	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637679	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13062423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13067095	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13067864	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13069355	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072751	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13073978	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13077766	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13084780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13093668	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095122	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13095125	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13098554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1546758	1.00[CEU][hapmap]
rs1563615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1625751	0.80[ASN][1000 genomes]
rs1672927	0.82[JPT][hapmap]
rs1672928	0.90[CHD][hapmap]
rs1672932	0.81[JPT][hapmap]
rs1673608	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1673622	0.82[JPT][hapmap]
rs1679181	0.81[JPT][hapmap]
rs1720829	0.80[JPT][hapmap]
rs1720833	0.80[ASN][1000 genomes]
rs2085446	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2085447	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2086351	0.80[ASN][1000 genomes]
rs2280596	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305269	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs34011134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153951	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34284415	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34316974	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34377792	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34416776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34482601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34583117	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34607531	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34640717	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34652182	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34878008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35034861	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35269190	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35270255	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35340237	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35489558	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35537868	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35549884	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35597846	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35834585	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35876758	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35906980	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3773748	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3813264	0.82[JPT][hapmap]
rs3884240	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3884241	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs497334	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs503922	0.82[JPT][hapmap]
rs529615	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs542010	0.81[CHB][hapmap]
rs56028542	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56654955	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57516770	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58873565	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59184769	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59371015	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60371967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60426689	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609797	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs61258082	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61662147	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6439809	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6439810	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs66775405	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67390774	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67666216	0.98[ASN][1000 genomes]
rs6768963	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs6784770	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645920	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs773450	0.82[JPT][hapmap]
rs774011	0.80[ASN][1000 genomes]
rs774012	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs811794	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs812277	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs814022	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs936316	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9848938	0.81[JPT][hapmap]
rs9855306	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9880928	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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
5	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9049	CEP70	cis	multi-tissue	Pritchard
rs9049	CEP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:138207000-138223800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:138208400-138227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:138208600-138215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:138208800-138213400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:138209200-138218400	Weak transcription	Gastric	stomach
7	chr3:138209400-138236800	Weak transcription	Aorta	Aorta
8	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:138210000-138218400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:138210000-138230200	Weak transcription	Fetal Brain Male	brain
11	chr3:138210200-138215000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:138210200-138222000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:138210400-138215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:138210400-138218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:138210400-138236800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:138210800-138214400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
19	chr3:138211000-138213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:138211000-138229400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:138211000-138231000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:138211000-138236600	Weak transcription	Spleen	Spleen
23	chr3:138211200-138213600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:138211200-138213600	Strong transcription	Liver	Liver
25	chr3:138211200-138213600	Strong transcription	Fetal Thymus	thymus
26	chr3:138211200-138215000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:138211200-138215000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:138211200-138215000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr3:138211200-138227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:138211200-138260600	Weak transcription	Brain Angular Gyrus	brain
31	chr3:138211400-138230400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:138211600-138213400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:138211600-138215200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:138211600-138227400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:138211800-138214400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:138211800-138214800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:138211800-138215200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:138211800-138260600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:138212000-138214400	Enhancers	NHDF-Ad	bronchial
40	chr3:138212000-138235000	Weak transcription	Brain Germinal Matrix	brain
41	chr3:138212000-138235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:138212200-138213600	Enhancers	HSMM	muscle
43	chr3:138212200-138214000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:138212200-138214200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:138212200-138214200	Enhancers	HMEC	breast
46	chr3:138212200-138214400	Enhancers	NHLF	lung
47	chr3:138212200-138218400	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:138212400-138214000	Weak transcription	Right Ventricle	heart
49	chr3:138212400-138214800	Weak transcription	Fetal Intestine Small	intestine
50	chr3:138212400-138215000	Weak transcription	Fetal Lung	lung

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