Variant report

Variant	rs12617050
Chromosome Location	chr2:127458455-127458456
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10174393	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10191577	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1050967	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1530149	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1964424	0.83[AMR][1000 genomes]
rs1968539	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165227	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2176428	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs2176429	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs2280238	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2280239	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2280240	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3791345	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56224235	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6431172	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709803	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6713909	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6732145	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71393823	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs893801	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs935022	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs935024	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs938733	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[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	nsv1002265	chr2:127029745-127733458	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535919	chr2:127029745-127733458	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583011	chr2:127386211-127489031	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12617050	LIMS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127443600-127458800	Strong transcription	Primary T cells from cord blood	blood
2	chr2:127451400-127458800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:127451400-127459000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:127453200-127461200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:127455000-127460800	Weak transcription	Pancreas	Pancrea
6	chr2:127455400-127459600	Weak transcription	Right Ventricle	heart
7	chr2:127455600-127460600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:127455800-127460000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:127455800-127462400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:127456000-127461400	Weak transcription	Esophagus	oesophagus
11	chr2:127456200-127458800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:127456200-127458800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:127456200-127459200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:127456200-127459200	Enhancers	Fetal Stomach	stomach
15	chr2:127456200-127459400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:127456200-127460800	Weak transcription	Lung	lung
17	chr2:127456200-127460800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:127456200-127462000	Weak transcription	Aorta	Aorta
19	chr2:127456200-127462800	Weak transcription	Gastric	stomach
20	chr2:127456400-127458800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:127456400-127459000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:127456400-127459600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:127456400-127460400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:127456400-127463600	Enhancers	Fetal Muscle Leg	muscle
25	chr2:127456400-127466200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:127456600-127459400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:127456600-127459400	Enhancers	Ovary	ovary
28	chr2:127456600-127460400	Enhancers	Adipose Nuclei	Adipose
29	chr2:127456600-127462200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:127456800-127459400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:127457000-127458800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr2:127457000-127460000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:127457000-127461000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:127457200-127458600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr2:127457200-127459000	Enhancers	Fetal Lung	lung
36	chr2:127457400-127458600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr2:127457400-127458800	Enhancers	Brain Germinal Matrix	brain
38	chr2:127457400-127458800	Enhancers	Fetal Kidney	kidney
39	chr2:127457400-127459200	Enhancers	Colon Smooth Muscle	Colon
40	chr2:127457400-127460200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:127457600-127458800	Enhancers	Brain Hippocampus Middle	brain
42	chr2:127457600-127458800	Enhancers	Right Atrium	heart
43	chr2:127457600-127458800	Enhancers	NHLF	lung
44	chr2:127457600-127461000	Weak transcription	Psoas Muscle	Psoas
45	chr2:127457800-127458600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr2:127457800-127459400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:127457800-127461400	Weak transcription	Spleen	Spleen
48	chr2:127458200-127458600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:127458200-127458800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:127458200-127459800	Weak transcription	Left Ventricle	heart

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