Variant report

Variant	rs12595927
Chromosome Location	chr16:69716338-69716339
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10048108	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10163235	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10454066	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10500551	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10852458	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11075730	0.84[ASN][1000 genomes]
rs11639947	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11641233	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11643530	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11646884	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12232410	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12447883	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12449005	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12595869	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12595878	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12596823	0.82[AMR][1000 genomes]
rs13337236	0.86[ASN][1000 genomes]
rs1437135	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437136	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16958970	0.80[EUR][1000 genomes]
rs16959025	0.82[EUR][1000 genomes]
rs16959035	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1800566	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1865965	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2118220	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2196574	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2217950	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2361838	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2361839	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3169315	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3743673	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3885612	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55701476	0.81[AMR][1000 genomes]
rs55751101	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56316408	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57488237	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57565297	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60010276	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60472033	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61310815	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61460899	0.84[ASN][1000 genomes]
rs6499239	0.86[ASN][1000 genomes]
rs689455	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7186002	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7198242	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72783115	0.88[ASN][1000 genomes]
rs74026882	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74029403	0.86[EUR][1000 genomes]
rs8045142	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8046314	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8047885	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8052086	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8053080	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8054000	0.84[ASN][1000 genomes]
rs8054096	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8060588	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs920191	0.86[ASN][1000 genomes]
rs9788803	0.86[ASN][1000 genomes]
rs9788837	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9921045	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9933526	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12595927	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69667000-69727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:69671200-69726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:69681600-69725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:69681600-69725800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:69685000-69724800	Weak transcription	Fetal Heart	heart
6	chr16:69688600-69725400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:69690200-69725800	Weak transcription	Ovary	ovary
8	chr16:69691000-69726400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:69694800-69719200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr16:69694800-69725800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr16:69700400-69725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr16:69701400-69717400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:69701400-69725600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr16:69701800-69739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr16:69702200-69716800	Strong transcription	HSMM	muscle
16	chr16:69703400-69717600	Weak transcription	Pancreas	Pancrea
17	chr16:69704000-69725400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:69704600-69737800	Strong transcription	Liver	Liver
19	chr16:69705800-69725800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr16:69705800-69725800	Weak transcription	Gastric	stomach
21	chr16:69705800-69725800	Weak transcription	Small Intestine	intestine
22	chr16:69705800-69726000	Weak transcription	Psoas Muscle	Psoas
23	chr16:69706000-69725000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:69706000-69726200	Weak transcription	Stomach Mucosa	stomach
25	chr16:69706200-69725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr16:69706200-69725800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:69706200-69725800	Weak transcription	Right Ventricle	heart
28	chr16:69706400-69725800	Weak transcription	Brain Angular Gyrus	brain
29	chr16:69708800-69739600	Strong transcription	Placenta	Placenta
30	chr16:69709000-69717400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:69709000-69739400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr16:69709200-69717600	Strong transcription	GM12878-XiMat	blood
33	chr16:69709200-69718000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr16:69709200-69719000	Strong transcription	HSMMtube	muscle
35	chr16:69709200-69720600	Strong transcription	Primary T cells from cord blood	blood
36	chr16:69709400-69716600	Strong transcription	Fetal Muscle Leg	muscle
37	chr16:69709400-69716600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr16:69709400-69716800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr16:69709400-69717400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:69709400-69720400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr16:69709400-69721600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr16:69709600-69717800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr16:69709600-69720800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr16:69709600-69721200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr16:69709600-69723600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:69709600-69724600	Strong transcription	Fetal Intestine Large	intestine
48	chr16:69709600-69726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr16:69709800-69717600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr16:69709800-69721600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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