Variant report

Variant	rs413078
Chromosome Location	chr21:40542695-40542696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40539973..40543967-chr21:40547698..40550109,4	MCF-7	breast:
2	chr21:40177627..40180426-chr21:40542526..40544967,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10154057	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1041439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11702268	0.90[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11910971	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13050247	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13050584	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13051430	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1541100	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs1541101	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1984748	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2026266	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2070867	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap]
rs2142111	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs2142117	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs2150410	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2150412	0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2183574	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2183575	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2183576	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2225425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2236437	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2245455	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2272576	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2272577	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2272578	0.89[EUR][1000 genomes]
rs2297258	0.89[EUR][1000 genomes]
rs2410104	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2410121	0.93[EUR][1000 genomes]
rs2735310	0.90[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs28399794	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs371625	0.83[ASN][1000 genomes]
rs377098	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs3831199	0.80[EUR][1000 genomes]
rs383967	1.00[ASW][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[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]
rs391062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414850	0.83[ASN][1000 genomes]
rs418298	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs418359	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs419469	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs425988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428602	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs429955	0.83[ASN][1000 genomes]
rs442972	0.83[ASN][1000 genomes]
rs444130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447988	1.00[ASW][hapmap]
rs452377	0.83[ASN][1000 genomes]
rs452776	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816619	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4816623	0.87[EUR][1000 genomes]
rs4817999	0.81[ASN][1000 genomes]
rs4818004	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4818006	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4818007	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4818011	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs4818012	0.93[EUR][1000 genomes]
rs55885019	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56151678	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517524	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6517525	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6517528	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap]
rs6517529	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6517530	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6517531	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6517532	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6517534	0.87[EUR][1000 genomes]
rs6517536	0.93[EUR][1000 genomes]
rs6517537	0.90[EUR][1000 genomes]
rs6517539	0.93[EUR][1000 genomes]
rs6517540	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs6517541	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs6650847	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66519408	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66746936	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67212994	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67382266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67649754	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68069991	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68086041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68114370	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718225	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs726046	0.90[CEU][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap]
rs7275773	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs7276559	0.93[EUR][1000 genomes]
rs7276698	0.93[EUR][1000 genomes]
rs7280149	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7281074	1.00[ASW][hapmap]
rs7282029	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7282604	0.85[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs7282724	0.93[EUR][1000 genomes]
rs7282947	1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7283439	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs7283652	0.93[EUR][1000 genomes]
rs760166	1.00[ASW][hapmap]
rs8127391	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs8127537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8128118	0.90[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs8129847	0.89[EUR][1000 genomes]
rs8130099	0.90[EUR][1000 genomes]
rs8130774	0.93[EUR][1000 genomes]
rs8130795	0.81[ASN][1000 genomes]
rs8131091	0.93[EUR][1000 genomes]
rs8131150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs8131263	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8131307	0.90[EUR][1000 genomes]
rs8132230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs914157	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs971229	0.93[EUR][1000 genomes]
rs973521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9975410	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9975614	0.84[EUR][1000 genomes]
rs9978591	0.89[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9978953	0.92[EUR][1000 genomes]
rs9979547	0.92[EUR][1000 genomes]
rs9981656	0.87[EUR][1000 genomes]
rs9982122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs413078	C21orf107	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40533600-40545400	Weak transcription	HUVEC	blood vessel
2	chr21:40537200-40542800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr21:40537200-40543000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr21:40537200-40543000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:40537200-40543000	Weak transcription	Lung	lung
6	chr21:40537200-40543000	Weak transcription	Pancreas	Pancrea
7	chr21:40537400-40543000	Weak transcription	Aorta	Aorta
8	chr21:40537400-40543000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:40537400-40543200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr21:40537600-40553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr21:40537800-40543000	Weak transcription	HepG2	liver
12	chr21:40538000-40543000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr21:40538200-40543200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr21:40538400-40542800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr21:40538400-40543000	Weak transcription	Fetal Intestine Small	intestine
16	chr21:40538400-40544800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr21:40538600-40543000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:40538600-40543000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:40538800-40542800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr21:40538800-40542800	Weak transcription	K562	blood
21	chr21:40538800-40543000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr21:40538800-40545200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr21:40538800-40550400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr21:40539000-40543000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr21:40539000-40543000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr21:40539000-40550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40539200-40542800	Weak transcription	Fetal Kidney	kidney
28	chr21:40539200-40543000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr21:40539200-40543400	Weak transcription	Brain Anterior Caudate	brain
30	chr21:40539400-40543000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:40539400-40544800	Weak transcription	NHDF-Ad	bronchial
32	chr21:40539400-40545200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr21:40539600-40554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr21:40539800-40554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr21:40540000-40543000	Weak transcription	Ovary	ovary
36	chr21:40540000-40543200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr21:40540200-40554200	Weak transcription	Psoas Muscle	Psoas
38	chr21:40540800-40543000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr21:40540800-40543000	Weak transcription	Brain Hippocampus Middle	brain
40	chr21:40540800-40543000	Weak transcription	Fetal Thymus	thymus
41	chr21:40540800-40543000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr21:40540800-40543000	Weak transcription	Spleen	Spleen
43	chr21:40541000-40543000	Weak transcription	Gastric	stomach
44	chr21:40541000-40543000	Weak transcription	Right Ventricle	heart
45	chr21:40541000-40543000	Weak transcription	Osteobl	bone
46	chr21:40541000-40543200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40541000-40543200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr21:40541000-40543200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr21:40541000-40543200	Weak transcription	NH-A	brain
50	chr21:40541000-40543800	Weak transcription	Colonic Mucosa	Colon

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