Variant report

Variant	rs2838797
Chromosome Location	chr21:46593248-46593249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46592424..46595013-chr21:46596357..46598792,2	MCF-7	breast:
2	chr21:46592578..46594651-chr21:46685178..46686890,2	MCF-7	breast:
3	chr21:46592718..46595098-chr21:46595762..46598236,3	K562	blood:

Variant related genes	Relation type
ENSG00000186866	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11088982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11088983	0.86[CEU][hapmap];0.94[CHB][hapmap]
rs12185823	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13047803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1537121	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556317	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003273	0.81[JPT][hapmap]
rs2150439	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838778	0.81[JPT][hapmap]
rs2838787	0.81[JPT][hapmap]
rs2838788	0.81[JPT][hapmap]
rs2838791	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2838803	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838820	0.84[MEX][hapmap]
rs28782181	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs365791	0.90[ASN][1000 genomes]
rs372766	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs374778	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs377524	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3788180	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs381466	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs384876	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs386762	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs407133	0.84[CEU][hapmap]
rs422720	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs427943	0.84[CEU][hapmap]
rs434492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs446158	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819030	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4819031	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6518214	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7281416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7281757	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8126717	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8126895	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128889	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8130224	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8133307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983749	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9974232	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	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

No data

Chromatin state (count:92 , 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	chr21:46563000-46595600	Weak transcription	Pancreas	Pancrea
3	chr21:46572200-46595600	Weak transcription	Brain Germinal Matrix	brain
4	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
5	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr21:46575000-46595600	Weak transcription	Dnd41	blood
7	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr21:46576200-46595800	Weak transcription	Fetal Lung	lung
10	chr21:46580400-46595600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:46582400-46595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr21:46582400-46595600	Weak transcription	Gastric	stomach
13	chr21:46582600-46598000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr21:46583800-46596200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr21:46583800-46606000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr21:46584000-46596600	Weak transcription	Brain Angular Gyrus	brain
17	chr21:46584400-46595600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr21:46587200-46596000	Weak transcription	Ovary	ovary
19	chr21:46587200-46600200	Weak transcription	Liver	Liver
20	chr21:46588000-46595600	Weak transcription	HMEC	breast
21	chr21:46588200-46604800	Weak transcription	NHLF	lung
22	chr21:46588600-46601000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr21:46588600-46601400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr21:46589000-46606400	Weak transcription	Brain Substantia Nigra	brain
25	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
26	chr21:46589200-46595400	Weak transcription	NH-A	brain
27	chr21:46589400-46595600	Weak transcription	Fetal Intestine Small	intestine
28	chr21:46589600-46595800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr21:46589600-46596000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:46589600-46604600	Weak transcription	Osteobl	bone
31	chr21:46589800-46595800	Weak transcription	Esophagus	oesophagus
32	chr21:46589800-46596200	Weak transcription	Colon Smooth Muscle	Colon
33	chr21:46589800-46596600	Weak transcription	Brain Anterior Caudate	brain
34	chr21:46589800-46596600	Weak transcription	Brain Hippocampus Middle	brain
35	chr21:46589800-46600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr21:46589800-46602400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr21:46589800-46604800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr21:46589800-46604800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr21:46590000-46596600	Weak transcription	Fetal Thymus	thymus
40	chr21:46590000-46604800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr21:46590000-46605000	Weak transcription	Psoas Muscle	Psoas
42	chr21:46590000-46608800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr21:46590800-46593800	Strong transcription	Hela-S3	cervix
44	chr21:46590800-46607000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr21:46591000-46605000	Strong transcription	HSMM	muscle
46	chr21:46591200-46594600	Strong transcription	HSMMtube	muscle
47	chr21:46591200-46595600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr21:46591200-46601600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr21:46591400-46593400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr21:46591400-46594400	Strong transcription	Primary T cells from cord blood	blood

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