Variant report

Variant	rs2008215
Chromosome Location	chr2:180040127-180040128
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180039372..180041323-chr2:180056705..180058266,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1048026	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10497533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10497534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892241	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105478	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs16866665	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866673	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17453976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17454024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17454108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17454150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454192	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454458	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1838872	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2028906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4101465	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4499457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58582728	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60072979	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61179885	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433759	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433766	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
3	chr2:179980000-180056800	Weak transcription	HSMM	muscle
4	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
5	chr2:179996200-180047600	Weak transcription	NH-A	brain
6	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
7	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
8	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
11	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
12	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
13	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
14	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
15	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
16	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
18	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
19	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
21	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
22	chr2:180015000-180041600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:180015000-180043200	Weak transcription	Gastric	stomach
24	chr2:180015000-180054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:180015000-180056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:180015000-180060600	Weak transcription	Lung	lung
27	chr2:180015200-180046200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:180015200-180047200	Weak transcription	Placenta	Placenta
29	chr2:180015400-180046000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:180015400-180049800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:180015400-180058000	Weak transcription	Fetal Stomach	stomach
32	chr2:180015400-180060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:180015800-180043400	Weak transcription	Liver	Liver
34	chr2:180016000-180049000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:180016000-180054200	Weak transcription	NHDF-Ad	bronchial
36	chr2:180016200-180054000	Weak transcription	Osteobl	bone
37	chr2:180023000-180052800	Weak transcription	Fetal Heart	heart
38	chr2:180024200-180045800	Weak transcription	GM12878-XiMat	blood
39	chr2:180024400-180048600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:180026400-180048800	Weak transcription	Fetal Intestine Small	intestine
41	chr2:180030400-180055400	Weak transcription	Thymus	Thymus
42	chr2:180030800-180046000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:180030800-180050800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:180031200-180052000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:180031400-180042200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:180031400-180050000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:180031800-180042000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:180031800-180042000	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:180031800-180045600	Weak transcription	Fetal Brain Female	brain
50	chr2:180032000-180040400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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