Variant report

Variant	rs2182295
Chromosome Location	chr10:27111627-27111628
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11015265	0.86[YRI][hapmap]
rs12413383	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12764628	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12774231	0.91[EUR][1000 genomes]
rs12776877	0.85[EUR][1000 genomes]
rs12779919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12780703	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16927314	0.83[YRI][hapmap]
rs16927334	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17669895	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17747961	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17748178	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018904	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094150	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2182294	0.93[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35175791	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35531360	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802614	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5010875	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5025734	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6482574	0.83[YRI][hapmap]
rs68021348	0.83[EUR][1000 genomes]
rs7091364	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7092571	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7092950	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7094825	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7096584	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7916104	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7920164	0.87[EUR][1000 genomes];0.84[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	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2182295	LYZL2	cis	parietal	SCAN
rs2182295	ABI1	cis	cerebellum	SCAN
rs2182295	PDSS1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27085600-27119000	Weak transcription	Fetal Lung	lung
2	chr10:27091800-27113200	Weak transcription	Placenta	Placenta
3	chr10:27093400-27112400	Weak transcription	Left Ventricle	heart
4	chr10:27095000-27130600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:27095000-27138600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr10:27095200-27119000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:27095400-27113000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:27095400-27116200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:27095400-27129800	Weak transcription	NHEK	skin
10	chr10:27095600-27114600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:27095600-27115400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr10:27095600-27129000	Weak transcription	Right Atrium	heart
13	chr10:27095600-27132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:27095600-27148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr10:27095800-27113400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr10:27096800-27112400	Weak transcription	Gastric	stomach
17	chr10:27097200-27120000	Weak transcription	HepG2	liver
18	chr10:27099000-27113800	Weak transcription	Fetal Brain Female	brain
19	chr10:27099800-27128800	Weak transcription	K562	blood
20	chr10:27101800-27129000	Weak transcription	Stomach Mucosa	stomach
21	chr10:27104800-27119200	Weak transcription	Esophagus	oesophagus
22	chr10:27104800-27129200	Weak transcription	Colonic Mucosa	Colon
23	chr10:27105000-27112400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:27105000-27122000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:27105200-27112600	Weak transcription	Small Intestine	intestine
26	chr10:27105400-27113400	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:27105800-27114000	Weak transcription	HSMM	muscle
28	chr10:27106000-27112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:27106000-27113800	Weak transcription	Liver	Liver
30	chr10:27106200-27113200	Weak transcription	Lung	lung
31	chr10:27106400-27112400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr10:27106600-27113000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr10:27106600-27119000	Weak transcription	Thymus	Thymus
34	chr10:27106600-27122000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:27107000-27129000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:27107400-27129000	Weak transcription	Spleen	Spleen
37	chr10:27107600-27114000	Weak transcription	Psoas Muscle	Psoas
38	chr10:27108000-27116400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr10:27108000-27120600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:27108200-27112200	Strong transcription	Fetal Thymus	thymus
41	chr10:27108400-27112000	Weak transcription	Brain Anterior Caudate	brain
42	chr10:27108400-27112600	Weak transcription	Brain Hippocampus Middle	brain
43	chr10:27108400-27113800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:27108600-27113000	Weak transcription	Adipose Nuclei	Adipose
45	chr10:27108800-27112000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:27108800-27112000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:27109200-27112600	Strong transcription	Primary T cells from cord blood	blood
48	chr10:27109400-27116200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr10:27109400-27132600	Weak transcription	HMEC	breast
50	chr10:27109600-27112000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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