Variant report

Variant	rs2839140
Chromosome Location	chr21:47616080-47616081
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	chr21:47609281..47613722-chr21:47615252..47618849,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160285	Chromatin interaction
ENSG00000235878	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10854480	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12482209	0.81[ASN][1000 genomes]
rs13046451	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13049175	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13052701	0.81[ASN][1000 genomes]
rs13052806	0.89[ASN][1000 genomes]
rs2001809	0.82[ASN][1000 genomes]
rs2187118	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187120	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187121	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187122	0.94[ASN][1000 genomes]
rs2254524	0.97[ASN][1000 genomes]
rs2277826	0.89[ASN][1000 genomes]
rs2280955	0.88[ASN][1000 genomes]
rs2280956	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280957	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280958	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280959	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2330408	0.96[ASN][1000 genomes]
rs2839139	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2839141	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2839144	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2839145	0.85[ASN][1000 genomes]
rs2839146	0.97[ASN][1000 genomes]
rs2839155	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839157	0.88[ASN][1000 genomes]
rs2839160	0.83[ASN][1000 genomes]
rs2839161	0.83[ASN][1000 genomes]
rs2839167	0.81[ASN][1000 genomes]
rs2968	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35679325	0.90[ASN][1000 genomes]
rs4818828	0.97[ASN][1000 genomes]
rs4819213	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819214	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4819215	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4819217	0.88[ASN][1000 genomes]
rs4819218	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55689527	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62212862	0.95[ASN][1000 genomes]
rs6518278	0.88[ASN][1000 genomes]
rs6518282	0.88[ASN][1000 genomes]
rs6518285	0.89[ASN][1000 genomes]
rs7280110	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282841	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs914247	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs915804	0.82[ASN][1000 genomes]
rs9717	0.94[ASN][1000 genomes]
rs9976233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979525	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9984242	0.88[ASN][1000 genomes]
rs9984708	0.83[ASN][1000 genomes]
rs9984986	0.89[ASN][1000 genomes]
rs999691	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
2	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
4	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
6	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	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
8	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
9	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv914098	chr21:47467894-47619784	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
17	nsv1061087	chr21:47476088-47643219	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
18	nsv1060978	chr21:47488073-47833640	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	n/a
19	nsv914101	chr21:47491014-47650362	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
20	nsv914116	chr21:47535248-47650362	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
21	nsv914132	chr21:47572244-47619784	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
22	nsv519904	chr21:47583506-47881309	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
23	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
24	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
25	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
26	nsv1062031	chr21:47608580-47643219	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
27	nsv933354	chr21:47609029-47851401	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2839140	MCM3AP-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2839140	C21orf56	Cis_1M	lymphoblastoid	RTeQTL
rs2839140	MCM3AP	cis	Skin Sun Exposed Lower leg	GTEx
rs2839140	YBEY	cis	Esophagus Mucosa	GTEx
rs2839140	YBEY	cis	Artery Tibial	GTEx
rs2839140	YBEY	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47605000-47633200	Weak transcription	Stomach Mucosa	stomach
2	chr21:47605200-47646200	Weak transcription	Psoas Muscle	Psoas
3	chr21:47605400-47625600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr21:47605400-47646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr21:47605400-47646200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr21:47605800-47621000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr21:47606600-47639800	Strong transcription	Fetal Brain Female	brain
8	chr21:47607400-47645200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr21:47607400-47646200	Strong transcription	Fetal Stomach	stomach
10	chr21:47607600-47617000	Strong transcription	Brain Germinal Matrix	brain
11	chr21:47607800-47621000	Strong transcription	Liver	Liver
12	chr21:47608400-47621000	Strong transcription	Dnd41	blood
13	chr21:47608400-47622800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr21:47609000-47617000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr21:47609000-47617600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:47609000-47634800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr21:47609200-47617000	Strong transcription	Spleen	Spleen
18	chr21:47609200-47621000	Strong transcription	Fetal Muscle Leg	muscle
19	chr21:47609400-47616400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr21:47609400-47617000	Strong transcription	Aorta	Aorta
21	chr21:47609400-47617200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:47609400-47618200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr21:47609400-47618200	Strong transcription	Colonic Mucosa	Colon
24	chr21:47609400-47621400	Weak transcription	A549	lung
25	chr21:47609400-47621600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr21:47609600-47617000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr21:47609600-47617000	Strong transcription	Ovary	ovary
28	chr21:47609600-47623000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr21:47609800-47617000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr21:47609800-47617600	Strong transcription	Brain Cingulate Gyrus	brain
31	chr21:47609800-47620000	Strong transcription	Lung	lung
32	chr21:47609800-47621000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr21:47609800-47621000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr21:47610000-47618200	Strong transcription	Fetal Intestine Small	intestine
35	chr21:47610000-47637600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr21:47610000-47644000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr21:47610200-47617000	Strong transcription	Fetal Intestine Large	intestine
38	chr21:47610200-47618200	Strong transcription	Brain Hippocampus Middle	brain
39	chr21:47610200-47618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr21:47610200-47621000	Strong transcription	Primary T cells from cord blood	blood
41	chr21:47610400-47616600	Strong transcription	Brain Angular Gyrus	brain
42	chr21:47610400-47616800	Strong transcription	Fetal Thymus	thymus
43	chr21:47610600-47616800	Strong transcription	Colon Smooth Muscle	Colon
44	chr21:47610800-47616800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr21:47610800-47616800	Strong transcription	Thymus	Thymus
46	chr21:47610800-47617000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr21:47610800-47617600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr21:47610800-47621000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr21:47611000-47617000	Strong transcription	Rectal Smooth Muscle	rectum
50	chr21:47611000-47617400	Strong transcription	Primary T cells fromperipheralblood	blood

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