Variant report

Variant	rs1356424
Chromosome Location	chr2:99425838-99425839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99425256..99428076-chr2:99429019..99431103,2	K562	blood:
2	chr2:99412276..99414413-chr2:99425331..99428982,3	MCF-7	breast:
3	chr2:99422357..99424127-chr2:99425278..99427119,2	MCF-7	breast:
4	chr2:99346314..99348268-chr2:99425170..99426808,2	MCF-7	breast:
5	chr2:99408029..99409823-chr2:99425187..99427144,2	MCF-7	breast:
6	chr2:99346420..99348928-chr2:99424461..99427357,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169003	0.83[EUR][1000 genomes]
rs10172158	0.80[EUR][1000 genomes]
rs10181972	0.83[EUR][1000 genomes]
rs10188156	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10189330	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11123755	0.80[EUR][1000 genomes]
rs11887536	0.80[EUR][1000 genomes]
rs12468024	0.80[EUR][1000 genomes]
rs12712033	0.85[JPT][hapmap]
rs12712035	0.91[CEU][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12712036	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs12712038	0.80[EUR][1000 genomes]
rs12992214	0.80[AMR][1000 genomes]
rs12999225	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs13004923	0.83[EUR][1000 genomes]
rs13389386	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1568213	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1581250	0.83[EUR][1000 genomes]
rs1581251	0.80[EUR][1000 genomes]
rs1878585	0.83[EUR][1000 genomes]
rs1983352	0.84[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2138082	0.84[EUR][1000 genomes]
rs2276604	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2280256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4263159	0.89[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4850888	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4851162	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4851163	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4851167	0.80[EUR][1000 genomes]
rs4851170	0.80[EUR][1000 genomes]
rs6542838	0.88[CEU][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6542839	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs6711022	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6713991	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6714243	0.80[EUR][1000 genomes]
rs6719634	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs6726156	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6757099	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579189	0.89[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7581128	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7582382	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7608889	0.80[EUR][1000 genomes]
rs9308815	0.81[ASN][1000 genomes]
rs981601	0.89[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs981602	0.88[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99409600-99426400	Weak transcription	Esophagus	oesophagus
2	chr2:99414000-99426600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:99418000-99442200	Weak transcription	Stomach Mucosa	stomach
4	chr2:99420800-99426800	Enhancers	Fetal Thymus	thymus
5	chr2:99421200-99427200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:99422800-99426600	Weak transcription	Aorta	Aorta
7	chr2:99423000-99426400	Weak transcription	Gastric	stomach
8	chr2:99423000-99432200	Weak transcription	Right Atrium	heart
9	chr2:99423200-99426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:99423200-99426400	Weak transcription	Fetal Intestine Large	intestine
11	chr2:99423200-99427000	Weak transcription	Fetal Kidney	kidney
12	chr2:99423400-99426400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:99423400-99439200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:99423600-99439200	Weak transcription	Brain Angular Gyrus	brain
15	chr2:99423800-99426600	Weak transcription	Spleen	Spleen
16	chr2:99423800-99434200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:99424000-99426200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:99424000-99426200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:99424000-99426200	Weak transcription	Fetal Lung	lung
20	chr2:99424000-99426600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:99424000-99426800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr2:99424000-99432000	Weak transcription	Right Ventricle	heart
23	chr2:99424000-99435600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:99424000-99438400	Weak transcription	Pancreas	Pancrea
25	chr2:99424400-99426000	Weak transcription	Brain Anterior Caudate	brain
26	chr2:99424600-99426000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr2:99424800-99434800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:99425000-99426000	Genic enhancers	Lung	lung
29	chr2:99425000-99426200	Weak transcription	HMEC	breast
30	chr2:99425000-99426400	Strong transcription	Fetal Intestine Small	intestine
31	chr2:99425400-99426000	Enhancers	Thymus	Thymus
32	chr2:99425400-99427200	Enhancers	HepG2	liver
33	chr2:99425600-99426000	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr2:99425600-99426600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:99425800-99426000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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