Variant report

Variant	rs2839640
Chromosome Location	chr21:44598568-44598569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44595798..44598770-chr21:45063265..45067849,4	MCF-7	breast:
2	chr21:44597633..44599530-chr21:44922531..44924601,2	MCF-7	breast:
3	chr21:44597167..44598866-chr21:44766112..44768773,2	MCF-7	breast:
4	chr21:44595975..44600241-chr21:44843202..44849395,11	MCF-7	breast:
5	chr21:44595827..44599164-chr21:44845631..44847666,4	MCF-7	breast:
6	chr21:44596302..44600320-chr21:44763162..44765941,4	MCF-7	breast:
7	chr21:44597096..44598685-chr21:44750362..44752904,2	MCF-7	breast:
8	chr21:44596910..44599943-chr21:44921245..44924609,4	MCF-7	breast:
9	chr21:44590676..44595436-chr21:44598084..44601687,4	K562	blood:
10	chr21:44597050..44598895-chr21:44866871..44869287,2	MCF-7	breast:
11	chr21:44595703..44598660-chr21:45028207..45031192,2	MCF-7	breast:
12	chr21:44588285..44592993-chr21:44594253..44598657,5	MCF-7	breast:
13	chr21:44598282..44598954-chr21:44689291..44689941,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction
ENSG00000237864	Chromatin interaction
ENSG00000160202	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1041453	0.90[EUR][1000 genomes]
rs11203177	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11702241	0.90[EUR][1000 genomes]
rs11909053	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11909888	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11910132	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11910213	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13048578	0.88[EUR][1000 genomes]
rs2839647	0.89[EUR][1000 genomes]
rs2839648	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28970980	0.93[EUR][1000 genomes]
rs28971677	0.93[EUR][1000 genomes]
rs7276182	0.89[EUR][1000 genomes]
rs7276342	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7280964	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913812	chr21:44213057-44686358	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription 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 miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv913828	chr21:44471692-44598827	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1067412	chr21:44526656-44772130	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
5	nsv1060276	chr21:44550394-44628579	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
7	nsv913832	chr21:44579105-44768562	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv587664	chr21:44585405-44598827	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	esv3440728	chr21:44595883-44600181	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv3427846	chr21:44597783-44602181	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv3430571	chr21:44598283-44602181	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv3369197	chr21:44598383-44602181	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44593800-44599000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr21:44593800-44599800	Enhancers	Placenta	Placenta
3	chr21:44593800-44601600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:44595600-44602400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr21:44596400-44599400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr21:44596400-44600400	Enhancers	Spleen	Spleen
7	chr21:44596600-44599200	Enhancers	Left Ventricle	heart
8	chr21:44596600-44599400	Enhancers	NHLF	lung
9	chr21:44596600-44599600	Enhancers	NHEK	skin
10	chr21:44596600-44600800	Enhancers	Pancreas	Pancrea
11	chr21:44596600-44601600	Enhancers	HMEC	breast
12	chr21:44596800-44599200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:44596800-44602400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr21:44597000-44598600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr21:44597000-44598600	Enhancers	Gastric	stomach
16	chr21:44597000-44598800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:44597000-44599200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr21:44597000-44599400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr21:44597000-44600000	Enhancers	Lung	lung
20	chr21:44597000-44601800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr21:44597200-44598800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr21:44597200-44599000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr21:44597200-44599400	Flanking Active TSS	HepG2	liver
24	chr21:44597200-44599600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr21:44597200-44601400	Enhancers	Brain Germinal Matrix	brain
26	chr21:44597400-44599200	Enhancers	Right Atrium	heart
27	chr21:44597400-44599400	Enhancers	Fetal Intestine Small	intestine
28	chr21:44597400-44599400	Enhancers	HSMM	muscle
29	chr21:44597400-44599600	Enhancers	Fetal Stomach	stomach
30	chr21:44597400-44599600	Enhancers	NH-A	brain
31	chr21:44597400-44600200	Enhancers	Right Ventricle	heart
32	chr21:44597600-44598800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr21:44597600-44599000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr21:44597600-44599000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:44597600-44599200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr21:44597600-44599400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr21:44597600-44599600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr21:44597600-44599600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr21:44597600-44599800	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr21:44597600-44601400	Enhancers	Fetal Brain Female	brain
41	chr21:44597600-44601600	Enhancers	Esophagus	oesophagus
42	chr21:44597800-44598600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr21:44597800-44598600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr21:44597800-44598800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:44597800-44598800	Flanking Active TSS	Fetal Lung	lung
46	chr21:44597800-44599000	Enhancers	Primary B cells from peripheral blood	blood
47	chr21:44597800-44599200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr21:44597800-44599200	Enhancers	Colonic Mucosa	Colon
49	chr21:44597800-44599200	Enhancers	Stomach Smooth Muscle	stomach
50	chr21:44597800-44599400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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