Variant report

Variant	rs6050198
Chromosome Location	chr20:24935048-24935049
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24932720..24935500-chr20:24938353..24940512,2	MCF-7	breast:
2	chr20:24934127..24936359-chr20:24972026..24973630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1056033	0.84[ASN][1000 genomes]
rs1056036	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11700073	0.85[CHB][hapmap]
rs11905625	0.85[CHB][hapmap]
rs12625319	0.82[ASN][1000 genomes]
rs13041643	0.84[ASN][1000 genomes]
rs1535042	0.85[CHB][hapmap]
rs2008275	1.00[CHB][hapmap]
rs2092565	0.84[ASN][1000 genomes]
rs2103736	0.84[ASN][1000 genomes]
rs2179729	0.84[ASN][1000 genomes]
rs2179730	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2206891	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2225459	0.84[ASN][1000 genomes]
rs2235847	1.00[CHB][hapmap]
rs227625	0.85[CHB][hapmap]
rs227633	0.85[CHB][hapmap]
rs227634	0.85[CHB][hapmap]
rs227650	0.82[CHB][hapmap]
rs227653	0.85[CHB][hapmap]
rs2387366	0.84[ASN][1000 genomes]
rs2387572	0.84[ASN][1000 genomes]
rs2892279	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34419834	0.84[ASN][1000 genomes]
rs4813541	0.84[ASN][1000 genomes]
rs4813542	0.84[ASN][1000 genomes]
rs4815337	0.84[ASN][1000 genomes]
rs4815339	0.82[ASN][1000 genomes]
rs4815340	0.84[ASN][1000 genomes]
rs4815341	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4815351	1.00[CHB][hapmap]
rs4815355	0.84[ASN][1000 genomes]
rs4815357	1.00[CHB][hapmap]
rs6050177	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6050179	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6050181	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6050201	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6083684	0.84[ASN][1000 genomes]
rs6083685	0.84[ASN][1000 genomes]
rs6083686	0.84[ASN][1000 genomes]
rs6083688	0.84[ASN][1000 genomes]
rs6083692	0.82[ASN][1000 genomes]
rs6083699	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6083709	1.00[CHB][hapmap]
rs6106975	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6114980	0.85[CHB][hapmap]
rs6114981	0.85[CHB][hapmap]
rs6114984	0.85[CHB][hapmap]
rs6132773	0.84[ASN][1000 genomes]
rs6132774	0.84[ASN][1000 genomes]
rs6132775	0.85[CHB][hapmap]
rs6132777	0.85[CHB][hapmap]
rs6132778	0.85[CHB][hapmap]
rs6138417	0.84[ASN][1000 genomes]
rs6138423	0.84[ASN][1000 genomes]
rs6138435	0.84[ASN][1000 genomes]
rs6138437	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6138442	0.85[CHB][hapmap]
rs6138453	1.00[CHB][hapmap]
rs6138455	0.85[CHB][hapmap]
rs6138457	0.85[CHB][hapmap]
rs6138458	0.85[CHB][hapmap]
rs6707	0.85[CHB][hapmap]
rs7268095	0.85[CHB][hapmap]
rs735886	0.84[ASN][1000 genomes]
rs8125909	0.85[CHB][hapmap]
rs8183891	1.00[CHB][hapmap]
rs926661	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs926662	0.84[ASN][1000 genomes]

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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS 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 target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6050198	APMAP	cis	Whole Blood	GTEx
rs6050198	CST7	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24928600-24940400	Weak transcription	Right Atrium	heart
2	chr20:24929600-24936400	Weak transcription	Fetal Intestine Small	intestine
3	chr20:24930000-24936400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:24930200-24936800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr20:24930200-24939400	Weak transcription	Right Ventricle	heart
6	chr20:24930400-24939000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:24930600-24935600	Weak transcription	Primary T cells from cord blood	blood
8	chr20:24930600-24943000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr20:24930800-24938200	Weak transcription	Colonic Mucosa	Colon
10	chr20:24931000-24938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:24931200-24936400	Weak transcription	Esophagus	oesophagus
12	chr20:24931200-24936400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr20:24931400-24939600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:24931600-24938000	Weak transcription	NHLF	lung
15	chr20:24931600-24938600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:24931800-24936400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr20:24932000-24943000	Weak transcription	HSMM	muscle
18	chr20:24932000-24943400	Weak transcription	HSMMtube	muscle
19	chr20:24932200-24941000	Weak transcription	A549	lung
20	chr20:24932400-24936000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr20:24932400-24936000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr20:24932600-24938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr20:24932600-24938200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:24932600-24939200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr20:24933000-24935600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:24933000-24936600	Weak transcription	Brain Anterior Caudate	brain
27	chr20:24933000-24937600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:24933200-24936400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr20:24933200-24936400	Weak transcription	Brain Germinal Matrix	brain
30	chr20:24933200-24937000	Weak transcription	Fetal Brain Female	brain
31	chr20:24933200-24940400	Weak transcription	Colon Smooth Muscle	Colon
32	chr20:24933400-24935600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr20:24933400-24936600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr20:24933400-24938000	Weak transcription	Left Ventricle	heart
35	chr20:24933400-24938600	Weak transcription	Aorta	Aorta
36	chr20:24933600-24935600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr20:24933600-24939000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr20:24933800-24935200	Genic enhancers	Fetal Muscle Leg	muscle
39	chr20:24933800-24936600	Weak transcription	Placenta	Placenta
40	chr20:24933800-24936800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:24933800-24937400	Weak transcription	HepG2	liver
42	chr20:24933800-24937400	Weak transcription	HMEC	breast
43	chr20:24933800-24941600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:24933800-24943800	Weak transcription	NHEK	skin
45	chr20:24934000-24936000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr20:24934000-24936400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr20:24934000-24936400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr20:24934000-24937000	Enhancers	Fetal Thymus	thymus
49	chr20:24934000-24937200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr20:24934000-24937200	Weak transcription	Duodenum Mucosa	Duodenum

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