Variant report

Variant	rs1109688
Chromosome Location	chr2:20804353-20804354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20803733..20805677-chr2:20834978..20836857,2	K562	blood:
2	chr2:20803088..20804929-chr2:20807955..20810549,2	K562	blood:
3	chr2:20792169..20793794-chr2:20803902..20806488,2	K562	blood:
4	chr2:20645830..20649178-chr2:20802657..20807893,7	MCF-7	breast:
5	chr2:20648867..20653601-chr2:20803677..20806150,6	MCF-7	breast:
6	chr2:20804020..20806157-chr2:20816542..20819817,4	MCF-7	breast:
7	chr2:20801916..20805511-chr2:20814938..20817926,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1047163	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1109689	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430232	1.00[ASN][1000 genomes]
rs16987893	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17718362	1.00[ASN][1000 genomes]
rs57417650	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60694842	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121969	1.00[ASN][1000 genomes]
rs62121970	1.00[ASN][1000 genomes]
rs72782382	1.00[ASN][1000 genomes]
rs72782389	1.00[ASN][1000 genomes]
rs72782390	1.00[ASN][1000 genomes]
rs72782397	1.00[ASN][1000 genomes]
rs72782400	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72784304	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72784309	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72784361	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active 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	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20796600-20804400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:20797000-20810600	Weak transcription	Colonic Mucosa	Colon
3	chr2:20797600-20810600	Weak transcription	Fetal Kidney	kidney
4	chr2:20797800-20804400	Weak transcription	Fetal Lung	lung
5	chr2:20797800-20804400	Weak transcription	NH-A	brain
6	chr2:20797800-20804400	Weak transcription	NHLF	lung
7	chr2:20797800-20810800	Weak transcription	Gastric	stomach
8	chr2:20799200-20804600	Weak transcription	Brain Germinal Matrix	brain
9	chr2:20799200-20809800	Weak transcription	Spleen	Spleen
10	chr2:20799400-20804600	Weak transcription	HMEC	breast
11	chr2:20799800-20804400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:20799800-20804600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:20799800-20808600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:20800000-20809200	Weak transcription	Aorta	Aorta
15	chr2:20800000-20809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:20800200-20808400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:20800400-20804400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:20800400-20804800	Weak transcription	Placenta	Placenta
19	chr2:20800400-20809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:20801000-20804800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:20801200-20808400	Weak transcription	HepG2	liver
22	chr2:20801800-20804400	Weak transcription	HUVEC	blood vessel
23	chr2:20802000-20804400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:20802800-20804400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:20802800-20804400	Weak transcription	NHEK	skin
26	chr2:20803200-20814000	Weak transcription	HSMM	muscle
27	chr2:20803600-20805400	Enhancers	Left Ventricle	heart
28	chr2:20803600-20806400	Enhancers	Colon Smooth Muscle	Colon
29	chr2:20803800-20804400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:20803800-20805200	Enhancers	Brain Substantia Nigra	brain
31	chr2:20803800-20805200	Enhancers	Fetal Muscle Trunk	muscle
32	chr2:20803800-20805200	Enhancers	Right Atrium	heart
33	chr2:20803800-20805800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:20804000-20804400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr2:20804000-20804400	Enhancers	Rectal Smooth Muscle	rectum
36	chr2:20804000-20804400	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:20804000-20804600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:20804000-20805200	Enhancers	Esophagus	oesophagus
39	chr2:20804000-20805200	Enhancers	Lung	lung
40	chr2:20804000-20805200	Enhancers	Psoas Muscle	Psoas
41	chr2:20804000-20805200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:20804000-20805400	Enhancers	Adipose Nuclei	Adipose
43	chr2:20804000-20805400	Enhancers	Fetal Muscle Leg	muscle
44	chr2:20804000-20805600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:20804000-20805800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr2:20804200-20804600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:20804200-20805000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:20804200-20805200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:20804200-20805200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:20804200-20805200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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