Variant report

Variant	rs12145243
Chromosome Location	chr1:86895847-86895848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10493790	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161810	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161812	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161814	0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11161816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161817	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161831	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs1158833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1182098	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1182099	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1182101	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12119411	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12123660	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12125965	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12130284	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12146009	0.91[CEU][hapmap]
rs12403033	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12406320	0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323036	0.85[AMR][1000 genomes]
rs1413431	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1413432	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17409213	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17409304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17449526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1814203	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs1931360	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1931361	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1931362	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs272486	0.84[AMR][1000 genomes]
rs272489	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs272490	0.81[ASN][1000 genomes]
rs272493	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272495	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272496	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272497	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272499	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272500	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs272501	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs272505	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs272506	0.84[AMR][1000 genomes]
rs272509	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs272512	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs272514	0.88[CEU][hapmap]
rs272515	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs272518	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35489949	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765983	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs421105	0.87[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs423991	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5026277	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56104000	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56408800	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57210989	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61124915	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688340	0.85[AMR][1000 genomes]
rs72720116	0.88[AMR][1000 genomes]
rs72720129	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs977919	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][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	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12145243	CLCA2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86890600-86903000	Weak transcription	Esophagus	oesophagus
2	chr1:86894200-86897400	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:86894400-86896200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:86894400-86896400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86894400-86896600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:86894400-86896600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:86894400-86896600	Enhancers	Dnd41	blood
8	chr1:86894400-86897000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:86894400-86900200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:86894600-86896600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:86894600-86896600	Enhancers	Osteobl	bone
12	chr1:86894800-86896000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:86894800-86896000	Enhancers	Fetal Thymus	thymus
14	chr1:86894800-86896200	Enhancers	Primary T cells from cord blood	blood
15	chr1:86894800-86896200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:86894800-86896200	Enhancers	Adipose Nuclei	Adipose
17	chr1:86894800-86896400	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:86894800-86896400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:86894800-86896400	Enhancers	NHLF	lung
20	chr1:86894800-86896600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:86894800-86897200	Enhancers	NHDF-Ad	bronchial
22	chr1:86895000-86896000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:86895000-86896000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:86895000-86896000	Enhancers	Fetal Lung	lung
25	chr1:86895000-86896000	Weak transcription	Placenta	Placenta
26	chr1:86895000-86896000	Weak transcription	Small Intestine	intestine
27	chr1:86895000-86896200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:86895000-86896200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:86895000-86896200	Enhancers	HSMM	muscle
30	chr1:86895000-86896400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:86895000-86896400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:86895000-86896600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:86895000-86896600	Enhancers	HUVEC	blood vessel
34	chr1:86895000-86898800	Weak transcription	Spleen	Spleen
35	chr1:86895200-86896200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:86895200-86896400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:86895200-86896600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:86895200-86896600	Enhancers	NH-A	brain
39	chr1:86895400-86896000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:86895400-86896000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:86895400-86896200	Enhancers	A549	lung
42	chr1:86895600-86896000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:86895600-86896000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:86895600-86896400	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr1:86895600-86896600	Enhancers	H9 Cell Line	embryonic stem cell
46	chr1:86895600-86896600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:86895800-86896000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:86895800-86896000	Enhancers	Ovary	ovary
49	chr1:86895800-86896000	Enhancers	HSMMtube	muscle
50	chr1:86895800-86896200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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