Variant report

Variant	rs377524
Chromosome Location	chr21:46581233-46581234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46570712..46573836-chr21:46580844..46582723,4	K562	blood:
2	chr21:46571989..46575021-chr21:46580299..46583331,3	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11088982	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11088983	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs12185823	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13047803	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1537121	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537122	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs1537123	0.85[CEU][hapmap]
rs1556317	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2003273	0.81[JPT][hapmap]
rs2150439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2225434	0.85[CEU][hapmap]
rs2246081	0.89[CEU][hapmap]
rs2838778	0.81[JPT][hapmap]
rs2838787	0.81[JPT][hapmap]
rs2838788	0.81[JPT][hapmap]
rs2838791	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2838797	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2838799	0.84[CEU][hapmap]
rs2838800	0.85[CEU][hapmap]
rs2838803	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2838806	0.88[CEU][hapmap]
rs2838807	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2838813	0.88[CEU][hapmap]
rs2838815	0.88[CEU][hapmap]
rs2849618	0.82[EUR][1000 genomes]
rs28782181	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs365791	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs367986	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs372766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs373037	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs374778	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs377902	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3788180	0.84[ASN][1000 genomes]
rs381466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs384876	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs394608	0.85[CEU][hapmap]
rs395761	0.85[CEU][hapmap]
rs397092	0.85[CEU][hapmap]
rs412646	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs421716	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs422720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs422870	0.81[EUR][1000 genomes]
rs434492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs446158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818766	0.88[CEU][hapmap]
rs4819030	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4819031	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6518214	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7281416	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7281757	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs8126717	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8126895	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8128889	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8130224	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs8133307	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8134789	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs983749	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs984791	0.85[CEU][hapmap]
rs9974232	0.84[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
rs377524	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr21:46568400-46581400	Weak transcription	Gastric	stomach
9	chr21:46569000-46587000	Weak transcription	NHEK	skin
10	chr21:46570400-46582600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr21:46572000-46584000	Weak transcription	Ovary	ovary
12	chr21:46572000-46584000	Weak transcription	Stomach Mucosa	stomach
13	chr21:46572200-46595600	Weak transcription	Brain Germinal Matrix	brain
14	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
15	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr21:46573000-46582800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr21:46573000-46588400	Weak transcription	Thymus	Thymus
18	chr21:46573600-46591800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr21:46573800-46586800	Weak transcription	Adipose Nuclei	Adipose
20	chr21:46574200-46589200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr21:46574800-46583600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr21:46575000-46586400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:46575000-46587000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr21:46575000-46595600	Weak transcription	Dnd41	blood
25	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr21:46575200-46581400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr21:46575200-46583600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:46575200-46586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr21:46575200-46587000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr21:46575400-46581400	Weak transcription	Fetal Thymus	thymus
31	chr21:46575400-46582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr21:46575400-46583200	Weak transcription	Right Atrium	heart
33	chr21:46575400-46583400	Weak transcription	Left Ventricle	heart
34	chr21:46575400-46583400	Weak transcription	Spleen	Spleen
35	chr21:46575400-46587800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr21:46575400-46588800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr21:46575400-46588800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr21:46575400-46589000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr21:46575600-46581600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr21:46575600-46581800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr21:46575600-46588800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr21:46575800-46583200	Weak transcription	Brain Angular Gyrus	brain
44	chr21:46576200-46582600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr21:46576200-46588800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr21:46576200-46595800	Weak transcription	Fetal Lung	lung
47	chr21:46577400-46582400	Genic enhancers	HSMMtube	muscle
48	chr21:46577400-46583400	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr21:46578000-46582000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr21:46578000-46583400	Weak transcription	Brain Inferior Temporal Lobe	brain

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