Variant report

Variant	rs6438552
Chromosome Location	chr3:119631814-119631815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119630695..119633017-chr3:119635093..119636918,2	K562	blood:
2	chr3:119621762..119624564-chr3:119631487..119633084,2	MCF-7	breast:
3	chr3:119630860..119633808-chr3:119813838..119816291,2	MCF-7	breast:
4	chr3:119629683..119632180-chr3:119812934..119815456,2	K562	blood:
5	chr3:119628793..119630341-chr3:119631140..119633914,2	K562	blood:
6	chr3:119629935..119635391-chr3:119636173..119640969,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10433404	0.87[JPT][hapmap]
rs10934500	0.87[JPT][hapmap]
rs10934502	0.87[JPT][hapmap]
rs10934503	0.86[JPT][hapmap]
rs10934505	0.87[JPT][hapmap]
rs10934506	0.87[JPT][hapmap]
rs10934507	0.85[JPT][hapmap]
rs1154595	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11915717	0.83[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs12630592	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[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs12634476	0.87[JPT][hapmap]
rs12634889	0.86[JPT][hapmap]
rs12638973	0.85[JPT][hapmap]
rs13321783	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546753	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1574154	0.87[JPT][hapmap]
rs1719890	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719891	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1719894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17204878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[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]
rs1732168	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1732170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17810676	0.81[ASN][1000 genomes]
rs1870931	0.87[JPT][hapmap]
rs1903765	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs2126583	0.84[ASN][1000 genomes]
rs2199503	0.91[JPT][hapmap]
rs2319398	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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2319399	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[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2472682	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs28536662	1.00[CEU][hapmap];0.91[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];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2873950	0.82[JPT][hapmap]
rs3107669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[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];0.81[ASN][1000 genomes]
rs334553	0.81[ASN][1000 genomes]
rs334563	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[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs3732359	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3732360	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3732361	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];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4261913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4340737	0.87[JPT][hapmap]
rs4491945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4624596	0.87[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4687892	0.82[ASN][1000 genomes]
rs4687893	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4688042	0.87[JPT][hapmap]
rs4688046	0.87[JPT][hapmap]
rs4688047	0.87[JPT][hapmap]
rs4688054	0.87[JPT][hapmap]
rs4688059	0.81[JPT][hapmap]
rs57695730	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58605236	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781942	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6784598	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];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6785049	1.00[CEU][hapmap];0.95[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];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792572	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];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795653	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];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796420	0.84[ASN][1000 genomes]
rs6800622	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];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805251	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808874	0.87[JPT][hapmap]
rs6808975	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7620750	0.82[CEU][hapmap]
rs7633279	0.87[JPT][hapmap]
rs7639388	0.91[JPT][hapmap]
rs7641045	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643875	0.81[AMR][1000 genomes]
rs7644234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[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];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9813864	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866394	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873477	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]
rs9878473	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];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9879295	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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
rs6438552	MUC13	cis	parietal	SCAN
rs6438552	GSK3B	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

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	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119608200-119639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
8	chr3:119611400-119632200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:119611400-119632200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:119611400-119634600	Weak transcription	Spleen	Spleen
11	chr3:119611400-119642000	Weak transcription	Fetal Brain Male	brain
12	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
14	chr3:119613000-119637400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:119614200-119645200	Weak transcription	K562	blood
16	chr3:119618400-119639800	Weak transcription	NHLF	lung
17	chr3:119620600-119635800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr3:119621200-119639600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:119621400-119632400	Strong transcription	Primary B cells from cord blood	blood
20	chr3:119621600-119632400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:119621800-119639000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:119622000-119633600	Weak transcription	Colonic Mucosa	Colon
23	chr3:119622200-119640800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:119624600-119634400	Weak transcription	HepG2	liver
25	chr3:119624600-119642200	Weak transcription	Brain Germinal Matrix	brain
26	chr3:119624800-119635400	Weak transcription	A549	lung
27	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
28	chr3:119625800-119635600	Weak transcription	Osteobl	bone
29	chr3:119626200-119633800	Strong transcription	Primary hematopoietic stem cells	blood
30	chr3:119627200-119634800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:119627600-119635000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:119627800-119632800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:119627800-119635200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:119627800-119640400	Weak transcription	Brain Substantia Nigra	brain
35	chr3:119628000-119636400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:119628200-119638800	Weak transcription	Aorta	Aorta
37	chr3:119628200-119643000	Weak transcription	Ovary	ovary
38	chr3:119628200-119643800	Weak transcription	Left Ventricle	heart
39	chr3:119628200-119655600	Weak transcription	Fetal Heart	heart
40	chr3:119628200-119663200	Weak transcription	Right Atrium	heart
41	chr3:119628400-119635600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:119628400-119651000	Weak transcription	Right Ventricle	heart
43	chr3:119628600-119632200	Weak transcription	Fetal Lung	lung
44	chr3:119628800-119635200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:119629400-119632800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:119629400-119634800	Strong transcription	NH-A	brain
47	chr3:119629400-119635000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:119629600-119632000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:119629600-119632200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach

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