Variant report

Variant	rs4915778
Chromosome Location	chr1:62263416-62263417
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62263282..62264953-chr1:62267149..62270089,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10889256	0.85[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs11207831	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207837	0.93[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11207842	0.88[EUR][1000 genomes]
rs11207844	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11580167	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038135	0.82[GIH][hapmap];0.87[TSI][hapmap]
rs12045055	0.82[EUR][1000 genomes]
rs12135784	0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs12403946	0.85[EUR][1000 genomes]
rs12407806	0.87[EUR][1000 genomes]
rs12755345	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3790576	0.91[EUR][1000 genomes]
rs3790577	0.85[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4418641	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4915777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915779	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4915781	0.88[EUR][1000 genomes]
rs4915782	0.86[EUR][1000 genomes]
rs61770137	0.90[EUR][1000 genomes]
rs6661185	0.88[EUR][1000 genomes]
rs7516332	0.85[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7519647	0.85[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7529082	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530529	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9645411	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62220200-62290200	Weak transcription	Lung	lung
2	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:62222000-62293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:62224000-62267600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:62224000-62290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:62225000-62284400	Weak transcription	Psoas Muscle	Psoas
7	chr1:62227800-62294600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
9	chr1:62231800-62273400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:62232800-62267200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:62233200-62263800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:62233400-62264200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:62233400-62288800	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:62235400-62288800	Weak transcription	A549	lung
15	chr1:62240200-62264600	Weak transcription	Right Ventricle	heart
16	chr1:62240800-62264800	Weak transcription	Hela-S3	cervix
17	chr1:62242200-62274400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:62243000-62270600	Weak transcription	Spleen	Spleen
19	chr1:62247600-62287400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:62247600-62297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:62250000-62302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:62251200-62268400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:62251200-62288600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:62251800-62272600	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:62252000-62275800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:62253000-62266600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:62253000-62274400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:62253600-62297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:62253800-62265400	Weak transcription	Fetal Kidney	kidney
31	chr1:62253800-62271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:62253800-62289000	Weak transcription	HepG2	liver
33	chr1:62254000-62286400	Weak transcription	Aorta	Aorta
34	chr1:62254000-62288600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:62254200-62288400	Weak transcription	Adipose Nuclei	Adipose
36	chr1:62254800-62263600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:62255400-62264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:62255600-62302400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:62257000-62291600	Weak transcription	Gastric	stomach
40	chr1:62257800-62265200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:62258400-62268800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:62260000-62275600	Weak transcription	Fetal Heart	heart
43	chr1:62260600-62264200	Strong transcription	NHEK	skin
44	chr1:62260800-62272000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:62261000-62265200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:62261000-62266200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:62261000-62266200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:62261400-62265800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:62261600-62265800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:62261600-62266000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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