Variant report

Variant	rs491602
Chromosome Location	chr12:121312331-121312332
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1067742	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774577	0.87[EUR][1000 genomes]
rs1105416	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065286	0.81[ASN][1000 genomes]
rs1151850	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1151851	0.87[ASN][1000 genomes]
rs1151852	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1151861	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151863	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151864	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1168945	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168954	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168956	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696361	0.86[EUR][1000 genomes]
rs1696363	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1718209	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1718211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1732395	0.87[EUR][1000 genomes]
rs1732396	0.87[EUR][1000 genomes]
rs1732398	0.87[EUR][1000 genomes]
rs1732405	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2454729	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs2649994	0.85[EUR][1000 genomes]
rs2649996	1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs2649998	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2650006	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs2701174	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2701178	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2701181	0.87[EUR][1000 genomes]
rs2701182	0.87[EUR][1000 genomes]
rs2948150	1.00[YRI][hapmap]
rs487310	0.84[ASN][1000 genomes]
rs487912	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs493811	0.84[ASN][1000 genomes]
rs497273	0.90[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs498230	0.82[ASN][1000 genomes]
rs509152	1.00[YRI][hapmap]
rs516978	0.84[AMR][1000 genomes]
rs520405	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs532140	1.00[YRI][hapmap]
rs532703	0.84[ASN][1000 genomes]
rs538785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550349	1.00[YRI][hapmap]
rs551087	1.00[YRI][hapmap]
rs564120	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs566704	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs566994	1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs568297	0.84[AMR][1000 genomes]
rs586305	1.00[YRI][hapmap]
rs589466	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs589699	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs594507	0.84[ASN][1000 genomes]
rs597203	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs618849	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs619679	0.97[ASN][1000 genomes]
rs620772	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs623857	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs628771	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6553	1.00[YRI][hapmap]
rs656933	0.98[ASN][1000 genomes]
rs662284	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs662739	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs674021	1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs679833	1.00[YRI][hapmap]
rs680303	0.84[ASN][1000 genomes]
rs683091	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683437	1.00[YRI][hapmap]
rs688402	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs694303	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7300722	0.87[EUR][1000 genomes]
rs791707	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs791713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763007	chr12:121309851-121317278	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs491602	UNQ1887	cis	Temporal Cortex	GTEx
rs491602	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs491602	SPPL3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121288000-121316600	Weak transcription	NHLF	lung
2	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
3	chr12:121291600-121312400	Weak transcription	Gastric	stomach
4	chr12:121292000-121312400	Weak transcription	Aorta	Aorta
5	chr12:121294200-121340400	Weak transcription	HSMM	muscle
6	chr12:121295000-121316200	Weak transcription	HMEC	breast
7	chr12:121297400-121339800	Weak transcription	A549	lung
8	chr12:121297600-121315200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:121298400-121313600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:121300600-121312400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:121300600-121328800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:121302000-121328800	Weak transcription	Fetal Intestine Large	intestine
13	chr12:121303400-121312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:121303600-121312400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:121303600-121312400	Weak transcription	Pancreas	Pancrea
16	chr12:121303800-121312400	Weak transcription	Lung	lung
17	chr12:121304200-121329800	Weak transcription	K562	blood
18	chr12:121304600-121339800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:121304800-121312600	Weak transcription	Stomach Mucosa	stomach
20	chr12:121304800-121322000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:121304800-121324200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:121305000-121317400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:121306000-121322800	Weak transcription	Primary B cells from cord blood	blood
24	chr12:121306200-121315000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:121306200-121319800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:121306600-121312400	Weak transcription	GM12878-XiMat	blood
27	chr12:121306600-121326600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:121306600-121331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:121308600-121316200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:121308800-121316600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:121308800-121323200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:121309200-121317000	Weak transcription	NHEK	skin
33	chr12:121309400-121313200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:121309800-121312600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr12:121310000-121312600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr12:121310200-121313000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:121310200-121313000	Enhancers	Brain Anterior Caudate	brain
38	chr12:121310200-121313400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:121310400-121312400	Weak transcription	Right Ventricle	heart
40	chr12:121310400-121317000	Weak transcription	HepG2	liver
41	chr12:121310600-121312400	Weak transcription	Brain Substantia Nigra	brain
42	chr12:121310600-121312400	Weak transcription	Ovary	ovary
43	chr12:121310600-121312400	Weak transcription	Psoas Muscle	Psoas
44	chr12:121310600-121312400	Weak transcription	Right Atrium	heart
45	chr12:121310600-121312400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:121310600-121312400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:121310600-121312400	Weak transcription	Spleen	Spleen
48	chr12:121310600-121312600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:121310600-121315200	Weak transcription	Fetal Stomach	stomach
50	chr12:121310800-121312400	Weak transcription	Colon Smooth Muscle	Colon

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