Variant report

Variant	rs2839289
Chromosome Location	chr21:47909726-47909727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47906669..47909833-chr21:47915665..47917888,4	K562	blood:
2	chr21:47903644..47905346-chr21:47909530..47912151,2	MCF-7	breast:
3	chr21:47908460..47910234-chr21:48023721..48026113,2	K562	blood:
4	chr21:47877136..47880459-chr21:47909304..47911302,3	K562	blood:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction
ENSG00000160307	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1010111	0.91[ASN][1000 genomes]
rs10854482	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11089076	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11701286	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11701512	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12627695	0.84[ASN][1000 genomes]
rs13047818	0.83[ASN][1000 genomes]
rs13049522	0.85[YRI][hapmap]
rs13050065	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13053115	0.85[ASN][1000 genomes]
rs17371795	0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs1981330	0.92[ASN][1000 genomes]
rs2016807	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2032110	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2078203	0.92[ASN][1000 genomes]
rs2330590	0.84[ASN][1000 genomes]
rs2330591	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2330592	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839224	0.85[YRI][hapmap]
rs2839251	1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2839262	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2839267	0.92[ASN][1000 genomes]
rs2839271	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2839273	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2839274	0.93[ASN][1000 genomes]
rs2839283	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2839292	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2839305	0.82[ASN][1000 genomes]
rs2839308	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4143362	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62224255	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71326328	0.87[ASN][1000 genomes]
rs7275926	0.85[ASN][1000 genomes]
rs7276409	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7277463	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7279052	1.00[YRI][hapmap]
rs7280077	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7282296	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7283381	0.83[AMR][1000 genomes]
rs762251	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8126917	0.86[ASN][1000 genomes]
rs8129188	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8130538	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8132320	0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8134014	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8134832	0.85[ASN][1000 genomes]
rs9637222	0.91[ASN][1000 genomes]
rs9637223	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9712582	0.88[ASN][1000 genomes]
rs9978195	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9979185	0.85[YRI][hapmap]
rs9979962	0.85[ASN][1000 genomes]
rs9981192	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9983522	0.88[ASN][1000 genomes]
rs9983528	1.00[YRI][hapmap]
rs9989933	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
2	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
3	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
4	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
5	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
6	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
7	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
10	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
11	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
12	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
14	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
15	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
16	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
18	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
19	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	30 gene(s)	inside rSNPs	n/a
20	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
23	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2839289	S100B	cis	Adipose Subcutaneous	GTEx
rs2839289	C21orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47880000-47916800	Weak transcription	Aorta	Aorta
2	chr21:47880200-47911600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr21:47880200-47916600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:47880400-47916600	Weak transcription	Fetal Kidney	kidney
5	chr21:47880400-47916600	Weak transcription	HSMMtube	muscle
6	chr21:47880400-47918000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:47880400-47918200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr21:47880400-47931200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr21:47889600-47918200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr21:47889800-47916800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr21:47890000-47909800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr21:47892800-47920200	Weak transcription	Small Intestine	intestine
13	chr21:47894800-47912800	Weak transcription	GM12878-XiMat	blood
14	chr21:47899000-47918000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr21:47899200-47916800	Weak transcription	Colon Smooth Muscle	Colon
16	chr21:47900800-47917000	Weak transcription	Colonic Mucosa	Colon
17	chr21:47903400-47918400	Weak transcription	Brain Substantia Nigra	brain
18	chr21:47903600-47910200	Weak transcription	Brain Anterior Caudate	brain
19	chr21:47903600-47912200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr21:47903600-47912200	Weak transcription	Brain Angular Gyrus	brain
21	chr21:47903600-47917000	Weak transcription	Brain Hippocampus Middle	brain
22	chr21:47903600-47918200	Weak transcription	Stomach Mucosa	stomach
23	chr21:47903600-47919200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr21:47904200-47911600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr21:47904200-47911600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr21:47904200-47918600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr21:47904200-47920200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr21:47904200-47920200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr21:47904200-47931200	Weak transcription	Psoas Muscle	Psoas
30	chr21:47904400-47918000	Weak transcription	Pancreas	Pancrea
31	chr21:47904600-47920200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr21:47904800-47918800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr21:47904800-47920200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr21:47905000-47920000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr21:47905000-47920600	Strong transcription	Placenta	Placenta
36	chr21:47905200-47919200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr21:47905400-47910400	Strong transcription	NHDF-Ad	bronchial
38	chr21:47905400-47919200	Strong transcription	Primary T cells from cord blood	blood
39	chr21:47905400-47919200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr21:47905800-47920200	Strong transcription	Liver	Liver
41	chr21:47906000-47914800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr21:47906200-47914800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr21:47906200-47920400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr21:47906600-47913000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr21:47906600-47913000	Strong transcription	Brain Germinal Matrix	brain
46	chr21:47906800-47918000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr21:47907000-47910000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr21:47907000-47912200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr21:47907000-47914200	Weak transcription	K562	blood
50	chr21:47907000-47918000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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