Variant report

Variant	rs2850329
Chromosome Location	chr4:102275264-102275265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10007821	0.84[EUR][1000 genomes]
rs10007902	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs10009249	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10017730	0.90[EUR][1000 genomes]
rs10027194	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1031033	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1031034	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1031035	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10433980	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10433981	0.91[EUR][1000 genomes]
rs10433982	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10433984	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11097747	0.89[EUR][1000 genomes]
rs1125180	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12499349	0.89[EUR][1000 genomes]
rs12642424	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649313	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13108283	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13109704	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13132496	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13135111	0.89[EUR][1000 genomes]
rs13135270	0.89[EUR][1000 genomes]
rs13135441	0.90[EUR][1000 genomes]
rs13143896	0.84[EUR][1000 genomes]
rs13148622	0.89[EUR][1000 genomes]
rs13148645	0.89[EUR][1000 genomes]
rs1348161	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1372242	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1441433	0.91[JPT][hapmap]
rs1476159	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1530259	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1549513	0.96[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1549514	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1549515	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1549516	0.96[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1583911	0.84[EUR][1000 genomes]
rs1596061	0.89[EUR][1000 genomes]
rs1822168	0.90[EUR][1000 genomes]
rs1822169	0.90[EUR][1000 genomes]
rs1946946	0.89[EUR][1000 genomes]
rs2044043	0.84[EUR][1000 genomes]
rs2044044	0.84[EUR][1000 genomes]
rs210811	0.89[EUR][1000 genomes]
rs2119591	0.87[EUR][1000 genomes]
rs2119592	0.89[EUR][1000 genomes]
rs2119593	0.89[EUR][1000 genomes]
rs2119595	0.81[EUR][1000 genomes]
rs2119596	0.89[EUR][1000 genomes]
rs2433297	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2433298	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2433299	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2433311	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583385	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2583386	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2583387	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2583389	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2583391	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583392	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583394	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2583395	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583397	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583399	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583400	0.86[JPT][hapmap]
rs2583401	0.82[JPT][hapmap]
rs2583406	0.91[JPT][hapmap]
rs2850326	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2850328	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850330	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850331	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850332	0.86[JPT][hapmap]
rs2850333	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850334	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2850344	0.86[JPT][hapmap]
rs2850350	0.82[JPT][hapmap]
rs2850351	0.86[JPT][hapmap]
rs2850354	0.86[JPT][hapmap]
rs2850355	0.90[JPT][hapmap]
rs2850356	0.90[JPT][hapmap]
rs2850366	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2850367	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850368	0.88[EUR][1000 genomes]
rs2850369	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2850370	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850371	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850372	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2850963	0.86[JPT][hapmap]
rs2850969	0.86[JPT][hapmap]
rs2850974	0.86[JPT][hapmap]
rs2850976	0.86[JPT][hapmap]
rs2866376	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28664200	0.90[EUR][1000 genomes]
rs293209	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs293210	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293211	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293213	0.89[EUR][1000 genomes]
rs293214	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293215	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293216	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs293217	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4235418	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4452435	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4574415	0.93[EUR][1000 genomes]
rs4698957	0.90[EUR][1000 genomes]
rs4699209	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4699210	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699211	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699212	0.90[EUR][1000 genomes]
rs4699213	0.90[EUR][1000 genomes]
rs4699214	0.90[EUR][1000 genomes]
rs61478357	0.83[EUR][1000 genomes]
rs6532928	0.90[EUR][1000 genomes]
rs6532929	0.89[EUR][1000 genomes]
rs6532930	0.89[EUR][1000 genomes]
rs6532934	0.89[EUR][1000 genomes]
rs6532935	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6816400	0.90[EUR][1000 genomes]
rs6824603	0.90[EUR][1000 genomes]
rs6825658	0.89[EUR][1000 genomes]
rs6845368	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6846097	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6847376	0.88[EUR][1000 genomes]
rs6852377	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6856370	0.90[EUR][1000 genomes]
rs755961	0.86[JPT][hapmap]
rs7668224	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7670594	0.89[EUR][1000 genomes]
rs7670922	0.85[EUR][1000 genomes]
rs7677595	0.89[EUR][1000 genomes]
rs7687487	0.91[EUR][1000 genomes]
rs7690316	0.84[EUR][1000 genomes]
rs833945	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833946	0.88[EUR][1000 genomes]
rs833948	0.89[EUR][1000 genomes]
rs833949	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs920559	0.81[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2850329	AP001816.1	cis	Whole Blood	GTEx
rs2850329	FLJ20021	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102270000-102276200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:102270000-102276600	Weak transcription	Ovary	ovary
3	chr4:102270000-102280800	Weak transcription	Aorta	Aorta
4	chr4:102271000-102276000	Weak transcription	Primary B cells from cord blood	blood
5	chr4:102271600-102276200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:102271600-102276600	Weak transcription	NHLF	lung
7	chr4:102271600-102277000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:102271600-102277000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:102271600-102277000	Weak transcription	Stomach Mucosa	stomach
10	chr4:102271600-102277000	Weak transcription	Hela-S3	cervix
11	chr4:102271600-102277200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:102271600-102277200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:102271800-102277200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:102272000-102275400	Weak transcription	NHEK	skin
15	chr4:102272000-102275600	Weak transcription	HMEC	breast
16	chr4:102272000-102276200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:102272000-102276600	Weak transcription	A549	lung
18	chr4:102272200-102276200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:102272200-102276200	Weak transcription	HepG2	liver

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