Variant report

Variant	rs2838817
Chromosome Location	chr21:46631698-46631699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46628488..46630403-chr21:46630969..46633237,2	K562	blood:
2	chr21:46618795..46620670-chr21:46629791..46632609,2	MCF-7	breast:
3	chr21:46624737..46628208-chr21:46629925..46633186,4	K562	blood:
4	chr21:46629696..46632039-chr21:46633272..46635087,2	K562	blood:
5	chr21:46626961..46628588-chr21:46630742..46633006,2	MCF-7	breast:
6	chr21:46629095..46632023-chr21:46643087..46645467,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2071873	0.94[ASN][1000 genomes]
rs2838808	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs373687	0.84[JPT][hapmap]
rs410184	0.83[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.88[MKK][hapmap]
rs414743	0.83[MEX][hapmap]
rs415597	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs419322	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription 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	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS 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	27 gene(s)	inside rSNPs	diseases
17	nsv587841	chr21:46619840-46647078	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838817	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
2	chr21:46606800-46640800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr21:46609600-46634600	Weak transcription	Fetal Heart	heart
4	chr21:46610000-46634800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr21:46610000-46644800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr21:46610200-46634400	Weak transcription	Psoas Muscle	Psoas
7	chr21:46610400-46641000	Weak transcription	Brain Germinal Matrix	brain
8	chr21:46610400-46641800	Weak transcription	HepG2	liver
9	chr21:46610800-46640200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr21:46610800-46641000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr21:46610800-46641200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr21:46610800-46647800	Weak transcription	Brain Angular Gyrus	brain
13	chr21:46611000-46639600	Weak transcription	Fetal Brain Male	brain
14	chr21:46611000-46639600	Weak transcription	Gastric	stomach
15	chr21:46611000-46644600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr21:46611000-46645000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr21:46617600-46632600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr21:46619000-46633000	Strong transcription	Stomach Smooth Muscle	stomach
19	chr21:46620800-46633600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr21:46621200-46633400	Strong transcription	HSMMtube	muscle
21	chr21:46621800-46640400	Weak transcription	Fetal Brain Female	brain
22	chr21:46622000-46640600	Weak transcription	Brain Substantia Nigra	brain
23	chr21:46622200-46632600	Strong transcription	Adipose Nuclei	Adipose
24	chr21:46622400-46635400	Strong transcription	Primary T cells from cord blood	blood
25	chr21:46622600-46632400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr21:46622800-46640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr21:46623000-46632400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr21:46623000-46633400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr21:46623200-46633800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr21:46623400-46632800	Strong transcription	Hela-S3	cervix
31	chr21:46623600-46634600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr21:46624600-46638600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr21:46625000-46632200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr21:46625000-46645000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr21:46625200-46640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr21:46625600-46639600	Weak transcription	Placenta	Placenta
37	chr21:46625600-46640800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr21:46625800-46632400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr21:46626000-46636600	Weak transcription	Brain Anterior Caudate	brain
40	chr21:46626600-46632400	Strong transcription	Left Ventricle	heart
41	chr21:46626600-46632600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr21:46626600-46633000	Strong transcription	Fetal Stomach	stomach
43	chr21:46626800-46632000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:46627200-46633200	Strong transcription	Fetal Muscle Leg	muscle
45	chr21:46628200-46639600	Weak transcription	NHEK	skin
46	chr21:46628400-46632200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr21:46628400-46632600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr21:46628600-46638000	Weak transcription	HMEC	breast
49	chr21:46628600-46640200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr21:46628600-46640400	Weak transcription	Esophagus	oesophagus

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