Variant report

Variant	rs464553
Chromosome Location	chr6:34315079-34315080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34309301..34312552-chr6:34312659..34315940,4	K562	blood:
2	chr6:34308267..34311502-chr6:34313780..34316538,3	K562	blood:
3	chr6:34314465..34317126-chr6:34317621..34320996,4	K562	blood:
4	chr6:34303886..34306765-chr6:34314497..34316952,3	K562	blood:
5	chr6:34305147..34308643-chr6:34314207..34316952,4	K562	blood:
6	chr6:34305355..34307280-chr6:34313931..34315752,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs16885998	0.83[CHD][hapmap]
rs16889706	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs169584	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1811968	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2006833	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs206919	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs206920	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs206921	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs206924	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs206925	0.82[EUR][1000 genomes]
rs206936	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs206941	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs206942	0.83[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2237098	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778077	0.82[JPT][hapmap]
rs3798556	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3798560	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798562	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs3913009	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs3913010	0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs410340	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs414739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs458576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587164	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711390	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs4713770	0.83[CHB][hapmap]
rs4713774	0.82[JPT][hapmap]
rs4713777	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs568502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57622072	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611928	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs62399909	0.83[ASN][1000 genomes]
rs6457773	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6907486	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6912971	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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6924482	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6924682	0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6924982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6925243	0.83[ASW][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs6930978	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7752035	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7757586	0.86[EUR][1000 genomes]
rs7757900	0.86[EUR][1000 genomes]
rs7765498	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9366856	0.82[EUR][1000 genomes]
rs9368810	0.81[AMR][1000 genomes]
rs9368813	0.86[EUR][1000 genomes]
rs9380433	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9380435	0.82[EUR][1000 genomes]
rs9394214	0.87[EUR][1000 genomes]
rs9394215	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9394218	0.82[EUR][1000 genomes]
rs9461981	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469775	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469779	0.87[EUR][1000 genomes]
rs9469780	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv1797588	chr6:34310476-34319041	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs464553	RPS10	cis	lymphoblastoid	seeQTL
rs464553	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34285200-34330600	Weak transcription	Thymus	Thymus
3	chr6:34285800-34326600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:34289000-34325200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:34298600-34326400	Weak transcription	A549	lung
6	chr6:34301600-34318000	Weak transcription	Fetal Brain Female	brain
7	chr6:34306000-34327800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:34306000-34328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:34307000-34320000	Weak transcription	Ovary	ovary
10	chr6:34308800-34330800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:34309200-34315800	Weak transcription	Placenta	Placenta
12	chr6:34309200-34318200	Weak transcription	Fetal Lung	lung
13	chr6:34309400-34317200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:34309400-34317800	Weak transcription	Brain Germinal Matrix	brain
15	chr6:34309600-34317200	Weak transcription	NHDF-Ad	bronchial
16	chr6:34309600-34319800	Weak transcription	Small Intestine	intestine
17	chr6:34309600-34329200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:34309800-34316800	Weak transcription	Osteobl	bone
19	chr6:34309800-34317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:34309800-34317000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:34309800-34317200	Weak transcription	HSMM	muscle
22	chr6:34309800-34318000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:34309800-34318000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:34309800-34318000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:34309800-34318000	Weak transcription	Fetal Intestine Small	intestine
26	chr6:34309800-34318600	Weak transcription	HMEC	breast
27	chr6:34309800-34320000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:34309800-34320000	Weak transcription	Pancreas	Pancrea
29	chr6:34309800-34320200	Weak transcription	HepG2	liver
30	chr6:34309800-34321400	Weak transcription	Lung	lung
31	chr6:34309800-34327000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:34309800-34329800	Weak transcription	Fetal Thymus	thymus
33	chr6:34309800-34330800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:34309800-34337600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:34309800-34347200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:34310000-34317000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:34310000-34318000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:34310000-34320200	Weak transcription	Fetal Stomach	stomach
39	chr6:34310000-34330600	Weak transcription	Dnd41	blood
40	chr6:34310200-34318000	Weak transcription	Liver	Liver
41	chr6:34310200-34318000	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:34310200-34318000	Weak transcription	NHLF	lung
43	chr6:34310200-34318200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:34310400-34318000	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:34310400-34320000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:34310400-34321600	Weak transcription	Right Ventricle	heart
47	chr6:34310400-34329200	Weak transcription	Brain Angular Gyrus	brain
48	chr6:34310600-34317200	Weak transcription	Fetal Heart	heart
49	chr6:34310600-34320000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:34310600-34326400	Weak transcription	Rectal Smooth Muscle	rectum

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