Variant report

Variant	rs6775574
Chromosome Location	chr3:113162095-113162096
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10934228	0.95[MEX][hapmap]
rs11715198	0.91[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12488964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091945	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17321330	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs1906142	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1979554	0.86[EUR][1000 genomes]
rs2054823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129430	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171293	0.96[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2895413	0.83[EUR][1000 genomes]
rs35581027	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35935366	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4682138	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682486	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55711506	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6438140	0.86[EUR][1000 genomes]
rs6438143	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6438144	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6438145	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438146	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6438147	0.96[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6438148	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66524865	0.82[EUR][1000 genomes]
rs6768117	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769970	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6777880	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6785962	0.86[EUR][1000 genomes]
rs6805201	0.82[CEU][hapmap]
rs6805691	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611694	0.90[CHB][hapmap]
rs7613082	0.85[CHB][hapmap]
rs7617772	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7618884	0.84[EUR][1000 genomes]
rs7621210	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623122	0.83[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7623389	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625841	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];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7631730	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633428	0.82[EUR][1000 genomes]
rs7642163	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7646985	0.82[AMR][1000 genomes]
rs7650538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775232	0.82[EUR][1000 genomes]
rs775233	0.84[EUR][1000 genomes]
rs9682734	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9815835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840124	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9848087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869141	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9870996	0.87[YRI][hapmap]
rs9874749	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6775574	WDR52	cis	parietal	SCAN
rs6775574	SIDT1	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113135200-113164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:113136000-113176400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:113145800-113166000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113145800-113176600	Weak transcription	Spleen	Spleen
6	chr3:113146000-113172000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:113146000-113191000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:113146200-113178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:113146400-113165000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:113147000-113165600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:113147400-113165400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:113147600-113162400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:113147800-113178800	Weak transcription	HSMM	muscle
14	chr3:113156000-113179400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:113159400-113163000	Strong transcription	A549	lung
16	chr3:113160200-113165000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:113160200-113167400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:113160200-113176000	Weak transcription	Gastric	stomach
19	chr3:113160200-113190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:113160400-113162200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:113160400-113164600	Weak transcription	Liver	Liver
22	chr3:113160400-113165000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:113160400-113176000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:113160400-113186800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:113160400-113188800	Weak transcription	Colonic Mucosa	Colon
26	chr3:113160400-113191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:113160400-113192800	Weak transcription	Stomach Mucosa	stomach
28	chr3:113160600-113162200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:113160600-113163000	Weak transcription	NHDF-Ad	bronchial
30	chr3:113160600-113165000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:113160600-113166200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:113160600-113168800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:113160600-113170800	Weak transcription	Lung	lung
34	chr3:113160600-113170800	Weak transcription	Pancreas	Pancrea
35	chr3:113160600-113172200	Weak transcription	Left Ventricle	heart
36	chr3:113160600-113178600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:113160600-113179200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:113160600-113181600	Weak transcription	Esophagus	oesophagus
39	chr3:113160600-113188600	Weak transcription	Psoas Muscle	Psoas
40	chr3:113160600-113190600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:113160600-113203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:113160800-113162200	Weak transcription	Primary B cells from cord blood	blood
43	chr3:113160800-113162200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:113160800-113163600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:113160800-113164000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:113160800-113164200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:113160800-113164600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:113160800-113164800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:113160800-113164800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:113160800-113164800	Weak transcription	Adipose Nuclei	Adipose

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