Variant report

Variant	rs9873477
Chromosome Location	chr3:119645976-119645977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119615199..119618060-chr3:119644767..119646419,2	K562	blood:
2	chr3:119640550..119642915-chr3:119645017..119647596,2	MCF-7	breast:
3	chr3:119643647..119646085-chr3:119668156..119670521,2	MCF-7	breast:
4	chr3:119640713..119642665-chr3:119644484..119646824,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10433404	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934500	0.87[JPT][hapmap]
rs10934502	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934503	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10934505	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934506	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934507	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1154595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11915717	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12630592	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs12634476	0.87[JPT][hapmap]
rs12634889	0.86[JPT][hapmap]
rs12638973	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs13321783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546753	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1574154	0.87[JPT][hapmap]
rs1719890	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1719891	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17204878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs1732168	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17810676	0.84[ASN][1000 genomes]
rs1870931	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1903765	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs2126583	0.86[ASN][1000 genomes]
rs2199503	0.91[JPT][hapmap]
rs2319398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2319399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472682	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs28536662	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2873950	0.82[JPT][hapmap]
rs3107669	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs334553	0.84[ASN][1000 genomes]
rs334563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs334564	0.81[ASN][1000 genomes]
rs3732359	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3732360	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs3732361	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4261913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4340737	0.87[JPT][hapmap]
rs4491945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4624596	0.87[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4687892	0.85[ASN][1000 genomes]
rs4687893	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4688042	0.87[JPT][hapmap]
rs4688046	0.87[JPT][hapmap]
rs4688047	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4688054	0.87[JPT][hapmap]
rs4688059	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs57695730	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58605236	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796420	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6800622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6805251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808874	0.87[JPT][hapmap]
rs6808975	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7620750	0.82[CEU][hapmap]
rs7633279	0.87[JPT][hapmap]
rs7639388	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7641045	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643875	0.81[AMR][1000 genomes]
rs7644234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9866394	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9879295	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9873477	GSK3B	cis	parietal	SCAN
rs9873477	MUC13	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119597600-119659000	Weak transcription	Gastric	stomach
3	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
5	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
7	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
8	chr3:119628200-119655600	Weak transcription	Fetal Heart	heart
9	chr3:119628200-119663200	Weak transcription	Right Atrium	heart
10	chr3:119628400-119651000	Weak transcription	Right Ventricle	heart
11	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
12	chr3:119630800-119663200	Weak transcription	Esophagus	oesophagus
13	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
14	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:119631200-119647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:119631200-119650400	Weak transcription	Small Intestine	intestine
17	chr3:119631400-119646200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:119631400-119660800	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:119631600-119656000	Weak transcription	NHEK	skin
20	chr3:119633400-119655600	Weak transcription	Fetal Kidney	kidney
21	chr3:119634000-119656200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:119635000-119649400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:119635000-119652000	Weak transcription	Adipose Nuclei	Adipose
24	chr3:119635000-119665400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:119635000-119667000	Weak transcription	Placenta	Placenta
26	chr3:119635400-119664600	Weak transcription	HMEC	breast
27	chr3:119636400-119667200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:119638800-119648200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:119638800-119655400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:119638800-119656000	Weak transcription	Primary T cells from cord blood	blood
31	chr3:119639400-119651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:119640000-119646800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:119640000-119649200	Weak transcription	Fetal Brain Female	brain
34	chr3:119640000-119649400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:119640000-119650600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:119640000-119663800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:119640200-119655800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:119640400-119649400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:119640400-119656000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:119640600-119649200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:119640600-119649200	Weak transcription	A549	lung
42	chr3:119640600-119664400	Weak transcription	HSMM	muscle
43	chr3:119640600-119665000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:119640600-119672400	Weak transcription	Osteobl	bone
45	chr3:119640800-119658000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:119640800-119665400	Weak transcription	Fetal Thymus	thymus
47	chr3:119641000-119648600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:119641000-119655400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:119641000-119661800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:119641000-119662600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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