Variant report

Variant	rs3788169
Chromosome Location	chr21:46580779-46580780
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	chr21:46578518..46581096-chr21:46581512..46584493,2	K562	blood:
2	chr21:46571989..46575021-chr21:46580299..46583331,3	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10222166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11911460	0.94[ASN][1000 genomes]
rs12482954	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12483020	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12483279	0.87[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12483288	0.94[ASN][1000 genomes]
rs12627065	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12627151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13433524	1.00[ASN][1000 genomes]
rs1556316	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1556318	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1556319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17004734	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap]
rs17004739	0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs17004743	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004748	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2838774	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap]
rs2838776	0.82[CHB][hapmap]
rs2838786	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838789	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap]
rs2838792	1.00[JPT][hapmap]
rs2838801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2838809	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2838810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2838811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2838812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2838814	0.94[ASN][1000 genomes]
rs2838816	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3178603	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs367228	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs372173	0.85[JPT][hapmap]
rs372549	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3746976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3788155	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3788156	0.89[ASW][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs3788163	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs3788164	0.92[JPT][hapmap]
rs3788170	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs386528	0.85[JPT][hapmap]
rs390504	0.85[JPT][hapmap]
rs398023	1.00[ASN][1000 genomes]
rs406551	0.85[JPT][hapmap]
rs412626	0.85[JPT][hapmap]
rs412666	0.85[JPT][hapmap]
rs421643	0.85[JPT][hapmap]
rs423726	0.85[JPT][hapmap]
rs428870	0.85[JPT][hapmap]
rs431529	0.85[JPT][hapmap]
rs431666	0.85[JPT][hapmap]
rs431775	0.85[JPT][hapmap]
rs437286	0.85[JPT][hapmap]
rs439884	0.85[JPT][hapmap]
rs442380	0.85[JPT][hapmap]
rs447656	0.85[JPT][hapmap]
rs454052	0.85[JPT][hapmap]
rs6518215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6518216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs6518217	0.94[ASN][1000 genomes]
rs6518218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs66664884	0.94[ASN][1000 genomes]
rs66837495	0.94[ASN][1000 genomes]
rs7277143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7279808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7283317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs731248	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs8127577	1.00[CEU][hapmap]
rs8129624	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8129934	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs8130097	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8132646	0.94[ASN][1000 genomes]
rs8132752	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs8134382	0.94[ASN][1000 genomes]
rs8134889	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs870145	0.90[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs870351	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs9653788	1.00[ASN][1000 genomes]
rs9978240	1.00[ASN][1000 genomes]
rs9978543	0.94[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

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46556600-46581000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
4	chr21:46557600-46582600	Weak transcription	Psoas Muscle	Psoas
5	chr21:46558600-46588800	Weak transcription	Colonic Mucosa	Colon
6	chr21:46560800-46586400	Weak transcription	Liver	Liver
7	chr21:46563000-46595600	Weak transcription	Pancreas	Pancrea
8	chr21:46566000-46583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr21:46568400-46581400	Weak transcription	Gastric	stomach
10	chr21:46569000-46587000	Weak transcription	NHEK	skin
11	chr21:46570400-46582600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr21:46571800-46580800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr21:46572000-46581000	Weak transcription	Fetal Brain Male	brain
14	chr21:46572000-46581200	Weak transcription	Lung	lung
15	chr21:46572000-46584000	Weak transcription	Ovary	ovary
16	chr21:46572000-46584000	Weak transcription	Stomach Mucosa	stomach
17	chr21:46572200-46595600	Weak transcription	Brain Germinal Matrix	brain
18	chr21:46572400-46581000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
20	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr21:46573000-46582800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr21:46573000-46588400	Weak transcription	Thymus	Thymus
23	chr21:46573600-46591800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:46573800-46586800	Weak transcription	Adipose Nuclei	Adipose
25	chr21:46574200-46589200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr21:46574800-46583600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:46575000-46581000	Weak transcription	Esophagus	oesophagus
28	chr21:46575000-46586400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:46575000-46587000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:46575000-46595600	Weak transcription	Dnd41	blood
31	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr21:46575200-46581400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr21:46575200-46583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr21:46575200-46586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr21:46575200-46587000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr21:46575400-46581400	Weak transcription	Fetal Thymus	thymus
37	chr21:46575400-46582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr21:46575400-46583200	Weak transcription	Right Atrium	heart
39	chr21:46575400-46583400	Weak transcription	Left Ventricle	heart
40	chr21:46575400-46583400	Weak transcription	Spleen	Spleen
41	chr21:46575400-46587800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr21:46575400-46588800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr21:46575400-46588800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr21:46575400-46589000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr21:46575600-46581600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr21:46575600-46581800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:46575600-46588800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr21:46575800-46583200	Weak transcription	Brain Angular Gyrus	brain
50	chr21:46576200-46580800	Weak transcription	H9 Cell Line	embryonic stem cell

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