Variant report

Variant	rs4277409
Chromosome Location	chr18:13241329-13241330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13218802..13221710-chr18:13239189..13241580,2	MCF-7	breast:
2	chr18:13238761..13241458-chr18:13244320..13246123,2	MCF-7	breast:
3	chr18:13237575..13239719-chr18:13241059..13243082,2	K562	blood:
4	chr18:13224896..13226941-chr18:13241101..13243122,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12458598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12607576	0.80[ASN][1000 genomes]
rs12955200	0.87[EUR][1000 genomes]
rs12968182	0.86[EUR][1000 genomes]
rs12968748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3901403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616353	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797744	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4797747	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797748	0.84[YRI][hapmap]
rs4797749	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4797750	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs55962651	0.80[ASN][1000 genomes]
rs56191278	0.80[ASN][1000 genomes]
rs59835474	0.82[ASN][1000 genomes]
rs62636871	0.80[ASN][1000 genomes]
rs6505789	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67772629	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7228009	0.81[EUR][1000 genomes]
rs7244519	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9944928	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9952186	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9952516	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9952649	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955376	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955747	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9958724	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9962328	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9967502	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223600-13241400	Weak transcription	Aorta	Aorta
2	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr18:13224400-13242600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr18:13224400-13245400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr18:13229400-13243000	Weak transcription	Dnd41	blood
8	chr18:13232800-13246200	Weak transcription	Psoas Muscle	Psoas
9	chr18:13233000-13241400	Enhancers	Fetal Brain Female	brain
10	chr18:13233000-13260200	Weak transcription	Colonic Mucosa	Colon
11	chr18:13233200-13245800	Weak transcription	Right Atrium	heart
12	chr18:13233400-13254000	Weak transcription	Spleen	Spleen
13	chr18:13233400-13259000	Weak transcription	Primary T cells from cord blood	blood
14	chr18:13233600-13243000	Weak transcription	Gastric	stomach
15	chr18:13235800-13245800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr18:13236200-13258800	Weak transcription	Fetal Lung	lung
17	chr18:13237400-13258800	Weak transcription	Adipose Nuclei	Adipose
18	chr18:13237400-13258800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr18:13237800-13258800	Weak transcription	Colon Smooth Muscle	Colon
20	chr18:13238600-13245200	Weak transcription	Fetal Heart	heart
21	chr18:13239400-13243000	Strong transcription	Thymus	Thymus
22	chr18:13239600-13255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr18:13240200-13244800	Strong transcription	Fetal Thymus	thymus
24	chr18:13240200-13246200	Weak transcription	Liver	Liver
25	chr18:13240200-13256000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:13240400-13241600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr18:13240400-13241600	Weak transcription	Fetal Stomach	stomach
28	chr18:13240400-13242000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr18:13240400-13243000	Weak transcription	Brain Germinal Matrix	brain
30	chr18:13240400-13246400	Weak transcription	Fetal Muscle Leg	muscle
31	chr18:13240600-13241600	Weak transcription	Brain Anterior Caudate	brain
32	chr18:13240600-13242800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr18:13240600-13243000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr18:13240600-13245200	Weak transcription	Left Ventricle	heart
35	chr18:13240600-13245600	Weak transcription	Right Ventricle	heart
36	chr18:13240600-13246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:13240600-13252400	Weak transcription	Brain Hippocampus Middle	brain
38	chr18:13240600-13252600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr18:13240800-13241600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:13240800-13241800	Weak transcription	Fetal Brain Male	brain
41	chr18:13240800-13245200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links