Variant report

Variant	rs394608
Chromosome Location	chr21:46581798-46581799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46571468..46573324-chr21:46581267..46583442,2	MCF-7	breast:
2	chr21:46570712..46573836-chr21:46580844..46582723,4	K562	blood:
3	chr21:46578518..46581096-chr21:46581512..46584493,2	K562	blood:
4	chr21:46571989..46575021-chr21:46580299..46583331,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11088983	0.82[CEU][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11700834	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13051236	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1537122	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1537123	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2225434	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2246081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838799	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838800	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838806	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838813	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838815	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838818	0.87[MEX][hapmap];0.80[MKK][hapmap]
rs2849618	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367986	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs372519	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs372766	0.85[CEU][hapmap]
rs373037	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs377524	0.85[CEU][hapmap]
rs377902	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788183	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs381466	0.81[CEU][hapmap]
rs386762	0.85[CEU][hapmap]
rs394872	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395761	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397092	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399185	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs403694	0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs407133	0.94[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs412646	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs414715	0.90[ASN][1000 genomes]
rs421716	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422720	0.85[CEU][hapmap]
rs422870	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs427943	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs446158	0.85[CEU][hapmap]
rs4818766	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4819034	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8134836	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs914206	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs983157	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs984791	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9980766	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	esv1802303	chr21:46580319-46606676	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs394608	C21orf58	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
3	chr21:46557600-46582600	Weak transcription	Psoas Muscle	Psoas
4	chr21:46558600-46588800	Weak transcription	Colonic Mucosa	Colon
5	chr21:46560800-46586400	Weak transcription	Liver	Liver
6	chr21:46563000-46595600	Weak transcription	Pancreas	Pancrea
7	chr21:46566000-46583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr21:46569000-46587000	Weak transcription	NHEK	skin
9	chr21:46570400-46582600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr21:46572000-46584000	Weak transcription	Ovary	ovary
11	chr21:46572000-46584000	Weak transcription	Stomach Mucosa	stomach
12	chr21:46572200-46595600	Weak transcription	Brain Germinal Matrix	brain
13	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
14	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr21:46573000-46582800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr21:46573000-46588400	Weak transcription	Thymus	Thymus
17	chr21:46573600-46591800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr21:46573800-46586800	Weak transcription	Adipose Nuclei	Adipose
19	chr21:46574200-46589200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr21:46574800-46583600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr21:46575000-46586400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr21:46575000-46587000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr21:46575000-46595600	Weak transcription	Dnd41	blood
24	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr21:46575200-46583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr21:46575200-46586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr21:46575200-46587000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr21:46575400-46582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr21:46575400-46583200	Weak transcription	Right Atrium	heart
30	chr21:46575400-46583400	Weak transcription	Left Ventricle	heart
31	chr21:46575400-46583400	Weak transcription	Spleen	Spleen
32	chr21:46575400-46587800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr21:46575400-46588800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr21:46575400-46588800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr21:46575400-46589000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr21:46575600-46581800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr21:46575600-46588800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr21:46575800-46583200	Weak transcription	Brain Angular Gyrus	brain
40	chr21:46576200-46582600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr21:46576200-46588800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr21:46576200-46595800	Weak transcription	Fetal Lung	lung
43	chr21:46577400-46582400	Genic enhancers	HSMMtube	muscle
44	chr21:46577400-46583400	Genic enhancers	Muscle Satellite Cultured Cells	--
45	chr21:46578000-46582000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr21:46578000-46583400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr21:46578000-46583600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr21:46578000-46583600	Weak transcription	HMEC	breast
49	chr21:46578800-46588800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr21:46579400-46582000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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