Variant report

Variant	rs600590
Chromosome Location	chr3:138349407-138349408
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	chr3:138324541..138329357-chr3:138346474..138351112,6	MCF-7	breast:
2	chr3:138337140..138340391-chr3:138349263..138352301,3	K562	blood:

Variant related genes	Relation type
ENSG00000158234	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1066197	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068104	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1068685	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804658	1.00[CHB][hapmap]
rs1091528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11720178	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs13069296	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433948	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1663554	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1663556	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1673597	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191713	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs191714	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs191775	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs2348147	0.81[AMR][1000 genomes]
rs2595928	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2595930	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2607796	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361057	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361059	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs361060	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs361061	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs361062	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361063	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs361066	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs361067	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361071	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs361072	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs361073	1.00[CHB][hapmap]
rs361074	1.00[CHB][hapmap]
rs361075	1.00[CHB][hapmap]
rs361076	1.00[CHB][hapmap]
rs361077	1.00[CHB][hapmap]
rs361080	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs361081	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs361082	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs361083	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs361084	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs361087	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs361088	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs361089	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361092	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361094	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs361096	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs361097	0.83[EUR][1000 genomes]
rs385254	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs413147	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4305444	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs439720	0.80[EUR][1000 genomes]
rs470359	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473388	0.83[AMR][1000 genomes]
rs475254	0.84[EUR][1000 genomes]
rs476800	0.83[AMR][1000 genomes]
rs484698	1.00[CHB][hapmap]
rs493152	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs497900	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs500687	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs520904	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs523975	1.00[CHB][hapmap]
rs524164	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs531577	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs537894	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap]
rs550768	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558905	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs559160	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559451	0.84[AMR][1000 genomes]
rs564455	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs589986	0.83[EUR][1000 genomes]
rs601032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs603723	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618457	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621204	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624099	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs625468	0.84[EUR][1000 genomes]
rs635592	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643620	1.00[CHB][hapmap]
rs647972	0.83[AMR][1000 genomes]
rs6784610	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs6795203	0.83[AMR][1000 genomes]
rs7641106	0.89[ASN][1000 genomes]
rs7643722	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs773045	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773184	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774015	1.00[CHB][hapmap]
rs811322	1.00[CHB][hapmap]
rs9821694	0.84[CEU][hapmap]
rs9822714	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9834963	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9864176	0.84[EUR][1000 genomes]
rs9879784	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	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	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
3	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
4	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
5	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
6	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
7	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
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs600590	ESYT3	cis	cerebellum	SCAN
rs600590	FAIM	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138328400-138350200	Weak transcription	Lung	lung
2	chr3:138328400-138353200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:138328400-138355000	Weak transcription	Esophagus	oesophagus
4	chr3:138328600-138358000	Weak transcription	Psoas Muscle	Psoas
5	chr3:138328800-138358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:138329000-138350000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:138329000-138354200	Weak transcription	Fetal Lung	lung
8	chr3:138335400-138368000	Weak transcription	Right Ventricle	heart
9	chr3:138337000-138360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:138337800-138353600	Weak transcription	Colonic Mucosa	Colon
11	chr3:138338000-138353400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:138338200-138350000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:138338600-138350400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:138339000-138351600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:138340400-138393800	Weak transcription	Fetal Brain Male	brain
16	chr3:138341000-138350600	Weak transcription	HepG2	liver
17	chr3:138341200-138351600	Weak transcription	Fetal Kidney	kidney
18	chr3:138341200-138355800	Weak transcription	Dnd41	blood
19	chr3:138341400-138349600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:138341400-138354600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:138341800-138355200	Weak transcription	Primary B cells from cord blood	blood
22	chr3:138342400-138362200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:138342600-138356400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:138343200-138352200	Weak transcription	Primary T cells from cord blood	blood
25	chr3:138343600-138352200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:138344800-138354000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:138345000-138354800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:138345000-138356600	Weak transcription	HSMMtube	muscle
29	chr3:138345000-138367800	Weak transcription	HSMM	muscle
30	chr3:138345200-138357600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:138345200-138357600	Weak transcription	Spleen	Spleen
32	chr3:138345400-138350600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:138345400-138352800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:138345400-138354200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:138345400-138355600	Weak transcription	NH-A	brain
36	chr3:138345400-138361600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:138345400-138368000	Weak transcription	NHLF	lung
38	chr3:138345600-138356600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:138345600-138367400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:138345800-138351000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:138345800-138354200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:138345800-138368000	Weak transcription	HMEC	breast
43	chr3:138346000-138354600	Weak transcription	NHEK	skin
44	chr3:138346400-138350000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:138346600-138356200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:138346600-138357800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:138347200-138352800	Weak transcription	Placenta	Placenta
48	chr3:138348000-138350800	Strong transcription	Brain Anterior Caudate	brain
49	chr3:138348000-138353000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:138348200-138351000	Strong transcription	Fetal Muscle Leg	muscle

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