Variant report

Variant	rs409322
Chromosome Location	chr20:25506220-25506221
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25504894..25507358-chr20:25508312..25510600,2	MCF-7	breast:
2	chr20:25503491..25506421-chr20:25552111..25554965,2	MCF-7	breast:
3	chr20:25487824..25490513-chr20:25503941..25506270,3	MCF-7	breast:

Extended variants
information (count: 169 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10485776	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109100	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12106173	0.83[EUR][1000 genomes]
rs1569617	0.82[AFR][1000 genomes]
rs16987786	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16987789	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16987799	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16987820	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16988014	0.81[EUR][1000 genomes]
rs1883528	0.82[AFR][1000 genomes]
rs2103661	0.82[AFR][1000 genomes]
rs2179458	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2388026	0.83[EUR][1000 genomes]
rs242133	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2424719	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2892408	0.84[AFR][1000 genomes]
rs35666277	0.91[ASN][1000 genomes]
rs3764695	0.83[EUR][1000 genomes]
rs400070	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409401	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4098823	0.83[EUR][1000 genomes]
rs4098824	0.83[EUR][1000 genomes]
rs4113658	0.83[EUR][1000 genomes]
rs4113659	0.83[EUR][1000 genomes]
rs4113662	0.83[EUR][1000 genomes]
rs426563	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs428278	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4343537	0.83[EUR][1000 genomes]
rs440612	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447808	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574179	0.83[EUR][1000 genomes]
rs4813570	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4815436	0.83[AFR][1000 genomes]
rs57638633	0.83[EUR][1000 genomes]
rs58169034	0.83[EUR][1000 genomes]
rs58184048	0.91[ASN][1000 genomes]
rs59324912	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59546510	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6037128	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6037131	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6037133	0.93[EUR][1000 genomes]
rs6037159	0.82[EUR][1000 genomes]
rs6037161	0.82[EUR][1000 genomes]
rs6037179	0.83[EUR][1000 genomes]
rs6037180	0.83[EUR][1000 genomes]
rs6037195	0.83[EUR][1000 genomes]
rs6037198	0.83[EUR][1000 genomes]
rs6037199	0.83[EUR][1000 genomes]
rs6037208	0.83[EUR][1000 genomes]
rs6037217	0.83[EUR][1000 genomes]
rs6037223	0.83[EUR][1000 genomes]
rs60394570	0.82[AFR][1000 genomes]
rs6050651	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6050658	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050663	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050692	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6050709	0.80[EUR][1000 genomes]
rs6050710	0.80[EUR][1000 genomes]
rs6050712	0.82[EUR][1000 genomes]
rs6050714	0.82[EUR][1000 genomes]
rs6050717	0.82[EUR][1000 genomes]
rs6050758	0.83[EUR][1000 genomes]
rs6050763	0.83[EUR][1000 genomes]
rs6050765	0.83[EUR][1000 genomes]
rs6050775	0.83[EUR][1000 genomes]
rs6050787	0.83[EUR][1000 genomes]
rs6050788	0.83[EUR][1000 genomes]
rs6050789	0.83[EUR][1000 genomes]
rs6050793	0.83[EUR][1000 genomes]
rs6050795	0.83[EUR][1000 genomes]
rs6050799	0.83[EUR][1000 genomes]
rs6050802	0.83[EUR][1000 genomes]
rs6050804	0.83[EUR][1000 genomes]
rs6050807	0.83[EUR][1000 genomes]
rs6050809	0.83[EUR][1000 genomes]
rs6050815	0.83[EUR][1000 genomes]
rs6050834	0.83[EUR][1000 genomes]
rs6050838	0.83[EUR][1000 genomes]
rs6050841	0.83[EUR][1000 genomes]
rs6050846	0.83[EUR][1000 genomes]
rs6050847	0.83[EUR][1000 genomes]
rs6050848	0.83[EUR][1000 genomes]
rs6050851	0.83[EUR][1000 genomes]
rs6050853	0.83[EUR][1000 genomes]
rs6050854	0.83[EUR][1000 genomes]
rs6076372	0.82[AFR][1000 genomes]
rs6083886	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6083896	0.82[AFR][1000 genomes]
rs6083899	0.82[AFR][1000 genomes]
rs6115220	0.84[AFR][1000 genomes]
rs6115224	0.82[AFR][1000 genomes]
rs6138608	0.81[AFR][1000 genomes]
rs6138612	0.82[AFR][1000 genomes]
rs6138613	0.82[AFR][1000 genomes]
rs66467007	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66591653	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66927803	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66940055	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67359112	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67455519	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67482703	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67679582	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67680401	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67921634	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68149491	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68165049	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7266130	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7266592	0.80[EUR][1000 genomes]
rs7274550	0.82[EUR][1000 genomes]
rs73337339	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73337343	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73337346	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73337349	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73337355	0.82[EUR][1000 genomes]
rs73337356	0.82[EUR][1000 genomes]
rs73337364	0.82[EUR][1000 genomes]
rs73337366	0.82[EUR][1000 genomes]
rs73337369	0.82[EUR][1000 genomes]
rs73337372	0.82[EUR][1000 genomes]
rs73337394	0.80[EUR][1000 genomes]
rs73339323	0.80[EUR][1000 genomes]
rs73339335	0.80[EUR][1000 genomes]
rs73339379	0.80[EUR][1000 genomes]
rs73341361	0.83[EUR][1000 genomes]
rs73343217	0.83[EUR][1000 genomes]
rs73343255	0.83[EUR][1000 genomes]
rs73345232	0.83[EUR][1000 genomes]
rs73345259	0.83[EUR][1000 genomes]
rs73345280	0.81[EUR][1000 genomes]
rs73597810	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73597811	0.97[ASN][1000 genomes]
rs73597812	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73597813	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742435	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742436	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8115484	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8115742	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8116267	0.81[EUR][1000 genomes]
rs8116474	0.85[EUR][1000 genomes]
rs8117181	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8117253	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8120594	0.82[EUR][1000 genomes]
rs8120972	0.82[EUR][1000 genomes]
rs8121648	0.83[EUR][1000 genomes]
rs8122516	0.85[EUR][1000 genomes]
rs8122589	0.80[EUR][1000 genomes]
rs8126111	0.82[EUR][1000 genomes]
rs926487	0.83[EUR][1000 genomes]
rs9753575	0.83[EUR][1000 genomes]
rs981440	0.83[EUR][1000 genomes]
rs981441	0.83[EUR][1000 genomes]
rs9941769	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs409322	RP4-694B14.5	cis	lung	GTEx
rs409322	RP4-694B14.5	cis	Stomach	GTEx
rs409322	RP4-694B14.5	cis	Adipose Subcutaneous	GTEx
rs409322	ZNF337	cis	Thyroid	GTEx
rs409322	ZNF337	cis	Stomach	GTEx
rs409322	ZNF337	cis	lung	GTEx
rs409322	ZNF337	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
2	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
3	chr20:25495800-25506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain
6	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
7	chr20:25496400-25506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:25497400-25512400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:25497400-25512400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr20:25497600-25506400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr20:25497600-25507200	Weak transcription	Colonic Mucosa	Colon
13	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
14	chr20:25497800-25506400	Weak transcription	HSMMtube	muscle
15	chr20:25497800-25512200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr20:25498000-25506400	Weak transcription	Fetal Brain Male	brain
17	chr20:25498000-25506600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr20:25498000-25511000	Weak transcription	Brain Hippocampus Middle	brain
19	chr20:25498200-25506600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr20:25498200-25506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr20:25498200-25507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:25498200-25507000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:25498200-25510800	Weak transcription	Brain Substantia Nigra	brain
24	chr20:25498200-25512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr20:25498200-25512200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr20:25498200-25512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr20:25498200-25512600	Weak transcription	Brain Anterior Caudate	brain
28	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
29	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
30	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
31	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr20:25498200-25519400	Weak transcription	Gastric	stomach
33	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr20:25499000-25507000	Weak transcription	Ovary	ovary
37	chr20:25501200-25507200	Strong transcription	Fetal Lung	lung
38	chr20:25501600-25507000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr20:25501600-25507200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr20:25502000-25507200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr20:25502000-25507600	Strong transcription	Dnd41	blood
42	chr20:25502400-25507200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr20:25502400-25507200	Strong transcription	Brain Germinal Matrix	brain
44	chr20:25502400-25507200	Strong transcription	Fetal Muscle Leg	muscle
45	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
46	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr20:25503000-25507400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr20:25503400-25507400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr20:25503400-25507400	Strong transcription	Thymus	Thymus
50	chr20:25503400-25508800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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