Variant report

Variant	rs72827739
Chromosome Location	chr2:99413514-99413515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99412895..99415398-chr2:99415733..99417676,2	MCF-7	breast:
2	chr2:99374384..99376088-chr2:99411488..99413627,2	MCF-7	breast:
3	chr2:99412276..99414413-chr2:99425331..99428982,3	MCF-7	breast:
4	chr2:99411307..99414136-chr2:99484785..99487668,2	MCF-7	breast:
5	chr2:99402708..99406014-chr2:99411806..99414792,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2090181	0.87[ASN][1000 genomes]
rs2203432	0.87[ASN][1000 genomes]
rs2871243	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871244	0.87[ASN][1000 genomes]
rs3731660	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851160	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs57185248	0.81[ASN][1000 genomes]
rs58516468	0.81[ASN][1000 genomes]
rs58560917	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58676789	0.89[ASN][1000 genomes]
rs59083513	0.87[ASN][1000 genomes]
rs59313126	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59989465	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60496162	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61042973	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61311613	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61359279	0.96[ASN][1000 genomes]
rs61402919	0.87[ASN][1000 genomes]
rs72811003	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72811004	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs72811005	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827717	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72827722	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72827724	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72827726	0.81[ASN][1000 genomes]
rs72827727	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72827729	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827731	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827732	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827733	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72827734	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72827736	0.85[ASN][1000 genomes]
rs72827740	0.87[ASN][1000 genomes]
rs72827741	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827742	0.87[ASN][1000 genomes]
rs72827743	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking 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	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99404400-99417200	Weak transcription	Stomach Mucosa	stomach
2	chr2:99406000-99421800	Weak transcription	Spleen	Spleen
3	chr2:99407600-99415800	Weak transcription	Left Ventricle	heart
4	chr2:99407600-99423800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:99409000-99415600	Weak transcription	Colonic Mucosa	Colon
6	chr2:99409200-99425800	Weak transcription	Small Intestine	intestine
7	chr2:99409400-99413800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr2:99409600-99426400	Weak transcription	Esophagus	oesophagus
9	chr2:99409800-99413600	Enhancers	HUVEC	blood vessel
10	chr2:99410600-99414000	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:99410600-99421600	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:99410800-99413600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:99411000-99415400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:99411200-99413600	Weak transcription	Placenta	Placenta
15	chr2:99411200-99415200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:99411200-99415400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:99411200-99415600	Weak transcription	Brain Substantia Nigra	brain
18	chr2:99411200-99421200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:99411200-99421200	Weak transcription	Right Atrium	heart
20	chr2:99411200-99422200	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:99411400-99415400	Weak transcription	HMEC	breast
22	chr2:99412000-99413800	Enhancers	Brain Anterior Caudate	brain
23	chr2:99412200-99414200	Enhancers	Fetal Thymus	thymus
24	chr2:99412400-99414600	Enhancers	Fetal Brain Male	brain
25	chr2:99412600-99413600	Genic enhancers	Fetal Intestine Small	intestine
26	chr2:99412600-99413800	Enhancers	Fetal Brain Female	brain
27	chr2:99412800-99413800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:99412800-99413800	Strong transcription	Pancreas	Pancrea
29	chr2:99412800-99414000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:99412800-99414000	Strong transcription	Gastric	stomach
31	chr2:99412800-99414600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr2:99412800-99421800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:99413000-99413600	Enhancers	Fetal Intestine Large	intestine
34	chr2:99413000-99413600	Weak transcription	Lung	lung
35	chr2:99413000-99415600	Enhancers	HepG2	liver
36	chr2:99413000-99417400	Weak transcription	Right Ventricle	heart
37	chr2:99413200-99413800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr2:99413200-99416600	Weak transcription	Liver	Liver
39	chr2:99413400-99413800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:99413400-99413800	ZNF genes & repeats	Thymus	Thymus
41	chr2:99413400-99414000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:99413400-99414200	Enhancers	Brain Cingulate Gyrus	brain

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