Variant report

Variant	rs11909888
Chromosome Location	chr21:44599081-44599082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44597633..44599530-chr21:44922531..44924601,2	MCF-7	breast:
2	chr21:44595975..44600241-chr21:44843202..44849395,11	MCF-7	breast:
3	chr21:44595827..44599164-chr21:44845631..44847666,4	MCF-7	breast:
4	chr21:44596302..44600320-chr21:44763162..44765941,4	MCF-7	breast:
5	chr21:44596910..44599943-chr21:44921245..44924609,4	MCF-7	breast:
6	chr21:44590676..44595436-chr21:44598084..44601687,4	K562	blood:
7	chr21:44598660..44599239-chr21:44846133..44847235,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1041453	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11203177	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11702241	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11909053	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11910132	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11910213	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13048578	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839640	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2839641	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2839642	0.82[ASN][1000 genomes]
rs2839643	0.82[ASN][1000 genomes]
rs2839647	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2839648	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28970980	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28971677	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919966	1.00[ASN][1000 genomes]
rs4919967	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7276182	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7276342	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280964	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44593800-44599800	Enhancers	Placenta	Placenta
2	chr21:44593800-44601600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:44595600-44602400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr21:44596400-44599400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr21:44596400-44600400	Enhancers	Spleen	Spleen
6	chr21:44596600-44599200	Enhancers	Left Ventricle	heart
7	chr21:44596600-44599400	Enhancers	NHLF	lung
8	chr21:44596600-44599600	Enhancers	NHEK	skin
9	chr21:44596600-44600800	Enhancers	Pancreas	Pancrea
10	chr21:44596600-44601600	Enhancers	HMEC	breast
11	chr21:44596800-44599200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:44596800-44602400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr21:44597000-44599200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr21:44597000-44599400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:44597000-44600000	Enhancers	Lung	lung
16	chr21:44597000-44601800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr21:44597200-44599400	Flanking Active TSS	HepG2	liver
18	chr21:44597200-44599600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr21:44597200-44601400	Enhancers	Brain Germinal Matrix	brain
20	chr21:44597400-44599200	Enhancers	Right Atrium	heart
21	chr21:44597400-44599400	Enhancers	Fetal Intestine Small	intestine
22	chr21:44597400-44599400	Enhancers	HSMM	muscle
23	chr21:44597400-44599600	Enhancers	Fetal Stomach	stomach
24	chr21:44597400-44599600	Enhancers	NH-A	brain
25	chr21:44597400-44600200	Enhancers	Right Ventricle	heart
26	chr21:44597600-44599200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr21:44597600-44599400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr21:44597600-44599600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr21:44597600-44599600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr21:44597600-44599800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr21:44597600-44601400	Enhancers	Fetal Brain Female	brain
32	chr21:44597600-44601600	Enhancers	Esophagus	oesophagus
33	chr21:44597800-44599200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr21:44597800-44599200	Enhancers	Colonic Mucosa	Colon
35	chr21:44597800-44599200	Enhancers	Stomach Smooth Muscle	stomach
36	chr21:44597800-44599400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr21:44597800-44599400	Enhancers	A549	lung
38	chr21:44597800-44599800	Enhancers	Fetal Muscle Leg	muscle
39	chr21:44597800-44600000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr21:44597800-44601400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:44598000-44599400	Weak transcription	Fetal Intestine Large	intestine
42	chr21:44598000-44599800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr21:44598000-44599800	Enhancers	Fetal Thymus	thymus
44	chr21:44598000-44600600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr21:44598000-44600800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr21:44598200-44599400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr21:44598200-44599400	Enhancers	Fetal Brain Male	brain
48	chr21:44598200-44599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr21:44598200-44599800	Enhancers	Hela-S3	cervix
50	chr21:44598200-44600000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links