Variant report

Variant	rs12375
Chromosome Location	chr1:10596341-10596342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PEX14-1	chr1:10596270-10596629	NONHSAT000859

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10864459	0.85[GIH][hapmap]
rs11121587	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1188526	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs12028449	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12402967	0.83[MKK][hapmap]
rs1411402	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035305	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026792	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056417	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2150038	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2480777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2480784	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2480785	0.90[EUR][1000 genomes]
rs2483677	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2506880	0.88[EUR][1000 genomes]
rs2506889	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2506892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2506896	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2506901	0.82[CEU][hapmap]
rs2781230	0.82[CEU][hapmap];0.93[GIH][hapmap]
rs2847344	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs34575776	0.97[EUR][1000 genomes]
rs4846235	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585870	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs589400	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs596537	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs607941	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs616402	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs616488	0.97[GIH][hapmap]
rs617728	0.90[EUR][1000 genomes]
rs620405	0.81[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs622623	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs636291	0.80[GIH][hapmap]
rs648324	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs648399	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs660725	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs662064	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.87[TSI][hapmap]
rs6687430	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs668805	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs669701	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs67488812	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9430149	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12375	AADACL3	cis	parietal	SCAN
rs12375	SLC2A5	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
2	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:10577400-10596400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:10584800-10603800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:10585200-10603600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:10585200-10603800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:10588400-10598200	Weak transcription	Pancreas	Pancrea
9	chr1:10588600-10596400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:10588800-10596400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:10588800-10599200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:10589000-10596400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:10589000-10600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:10589200-10598600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:10589400-10596400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
17	chr1:10590200-10596400	Weak transcription	Gastric	stomach
18	chr1:10590200-10597200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:10590200-10602800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:10590200-10605200	Weak transcription	NHDF-Ad	bronchial
21	chr1:10590600-10599400	Weak transcription	GM12878-XiMat	blood
22	chr1:10590800-10596400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:10590800-10598600	Weak transcription	Right Atrium	heart
24	chr1:10590800-10599800	Weak transcription	Right Ventricle	heart
25	chr1:10590800-10601000	Weak transcription	A549	lung
26	chr1:10591000-10596400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:10591000-10596400	Weak transcription	Adipose Nuclei	Adipose
28	chr1:10591000-10600200	Weak transcription	HUVEC	blood vessel
29	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
30	chr1:10591200-10596400	Weak transcription	Liver	Liver
31	chr1:10591200-10597400	Weak transcription	Fetal Thymus	thymus
32	chr1:10591200-10599200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:10591200-10599200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:10591200-10601000	Weak transcription	Placenta	Placenta
35	chr1:10591200-10601400	Weak transcription	Colonic Mucosa	Colon
36	chr1:10591400-10596400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:10591400-10596400	Weak transcription	NHLF	lung
38	chr1:10591400-10599600	Weak transcription	Fetal Kidney	kidney
39	chr1:10591400-10599600	Weak transcription	Ovary	ovary
40	chr1:10591400-10609000	Weak transcription	Small Intestine	intestine
41	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:10591600-10596400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:10591600-10596400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:10591600-10599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:10591800-10596400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:10591800-10596400	Weak transcription	Osteobl	bone
48	chr1:10592000-10596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:10592000-10598600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:10592000-10598600	Weak transcription	Stomach Smooth Muscle	stomach

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