Variant report

Variant	rs7633708
Chromosome Location	chr3:51381199-51381200
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	chr3:51376546..51378472-chr3:51379958..51381603,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1031925	0.84[CEU][hapmap]
rs10433609	0.95[CHB][hapmap]
rs11130280	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs11130286	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs11130290	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs11706571	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs12632046	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1318649	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap]
rs1383251	0.84[CEU][hapmap]
rs1480353	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1480360	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.80[YRI][hapmap]
rs1480362	0.95[CHB][hapmap]
rs1480364	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs1542574	0.84[CEU][hapmap];0.83[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2061950	0.95[CHB][hapmap];0.80[YRI][hapmap]
rs2101055	0.81[ASN][1000 genomes]
rs2164599	0.83[ASN][1000 genomes]
rs2170178	0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2219890	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2219891	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2241784	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2355943	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2883809	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2883812	0.81[ASN][1000 genomes]
rs3856932	0.90[CHB][hapmap]
rs4367100	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs4475072	0.90[CHB][hapmap]
rs4560329	0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs4687800	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4927970	0.95[CHB][hapmap]
rs4974092	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974094	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974099	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974104	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4974105	0.84[CEU][hapmap]
rs4974108	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs6445549	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445601	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs6445604	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs6445611	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs6445620	0.84[CEU][hapmap]
rs6445622	0.91[CEU][hapmap]
rs6445628	0.84[CEU][hapmap]
rs6445727	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6772668	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6784455	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6787805	0.95[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap]
rs6796847	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs751075	0.83[CEU][hapmap]
rs7614317	0.94[CHB][hapmap]
rs7616967	1.00[CHB][hapmap]
rs7617533	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7625006	0.84[CEU][hapmap]
rs7625821	0.83[ASN][1000 genomes]
rs7630714	0.82[ASN][1000 genomes]
rs7634799	0.95[CHB][hapmap]
rs7640083	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs7648012	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649069	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs7651141	1.00[CHB][hapmap]
rs899750	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap]
rs9832672	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9844581	0.95[CHB][hapmap]
rs9856566	1.00[CHB][hapmap]
rs9860403	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9877188	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs995543	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]

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	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7633708	TEX264	cis	Esophagus Muscularis	GTEx
rs7633708	TEX264	cis	Nerve Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
2	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:51378200-51383000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:51378400-51382600	Weak transcription	Spleen	Spleen
7	chr3:51378400-51389800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:51378600-51383000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:51378800-51381200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:51378800-51381400	Weak transcription	Esophagus	oesophagus
12	chr3:51378800-51381600	Weak transcription	Gastric	stomach
13	chr3:51378800-51381600	Weak transcription	Stomach Mucosa	stomach
14	chr3:51378800-51382000	Enhancers	Hela-S3	cervix
15	chr3:51378800-51383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:51378800-51387400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:51378800-51388000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
19	chr3:51379000-51381400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:51379000-51381400	Weak transcription	NHEK	skin
21	chr3:51379000-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:51379000-51386000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
26	chr3:51379200-51381200	Weak transcription	NHDF-Ad	bronchial
27	chr3:51379200-51381400	Weak transcription	HMEC	breast
28	chr3:51379200-51381600	Weak transcription	NH-A	brain
29	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:51379400-51381200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:51379400-51381400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:51379400-51381400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:51379400-51381400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:51379400-51382200	Weak transcription	Placenta	Placenta
37	chr3:51379400-51383800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:51379600-51381200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:51379600-51381200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:51379600-51381200	Weak transcription	HSMM	muscle
42	chr3:51379600-51381400	Weak transcription	Osteobl	bone
43	chr3:51379800-51381800	Strong transcription	Fetal Brain Female	brain
44	chr3:51379800-51382200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr3:51380000-51381200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:51380000-51381200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:51380000-51381200	Weak transcription	HSMMtube	muscle
48	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
50	chr3:51380200-51383000	Enhancers	A549	lung

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