Variant report

Variant	rs12129933
Chromosome Location	chr1:212984475-212984476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10127512	0.83[EUR][1000 genomes]
rs10127703	0.83[EUR][1000 genomes]
rs10127756	0.83[EUR][1000 genomes]
rs1046083	0.83[EUR][1000 genomes]
rs10863997	0.83[EUR][1000 genomes]
rs11120007	0.83[EUR][1000 genomes]
rs11120017	0.83[EUR][1000 genomes]
rs11120029	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120030	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120035	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120036	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11556187	0.84[EUR][1000 genomes]
rs11800642	0.83[EUR][1000 genomes]
rs11805669	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11806535	0.83[EUR][1000 genomes]
rs11809232	0.84[EUR][1000 genomes]
rs11809382	0.85[EUR][1000 genomes]
rs11811017	0.83[EUR][1000 genomes]
rs12036054	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12128410	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12128903	0.81[EUR][1000 genomes]
rs12130072	1.00[ASN][1000 genomes]
rs12133124	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12136656	0.96[ASN][1000 genomes]
rs12137768	0.83[EUR][1000 genomes]
rs12409787	0.87[ASN][1000 genomes]
rs13376317	0.85[EUR][1000 genomes]
rs13376383	0.85[EUR][1000 genomes]
rs13376390	0.85[EUR][1000 genomes]
rs1507357	0.83[EUR][1000 genomes]
rs1532951	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17019726	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2358899	0.83[EUR][1000 genomes]
rs34110137	0.84[EUR][1000 genomes]
rs3738803	0.85[EUR][1000 genomes]
rs55840547	0.83[EUR][1000 genomes]
rs56088044	0.85[EUR][1000 genomes]
rs56243109	0.83[EUR][1000 genomes]
rs59231663	0.81[EUR][1000 genomes]
rs60308869	0.83[EUR][1000 genomes]
rs6540760	0.83[EUR][1000 genomes]
rs6670648	0.83[EUR][1000 genomes]
rs6671866	0.85[EUR][1000 genomes]
rs6687672	0.83[EUR][1000 genomes]
rs6688238	0.83[EUR][1000 genomes]
rs6694190	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694448	0.83[EUR][1000 genomes]
rs73081853	0.83[EUR][1000 genomes]
rs73081902	0.83[EUR][1000 genomes]
rs73083707	0.82[EUR][1000 genomes]
rs73083727	0.85[EUR][1000 genomes]
rs73083731	0.85[EUR][1000 genomes]
rs73083749	0.83[EUR][1000 genomes]
rs73083756	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73083765	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73083778	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516312	0.83[EUR][1000 genomes]
rs7519582	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7527216	0.81[EUR][1000 genomes]
rs7538755	0.83[EUR][1000 genomes]
rs7546754	0.82[EUR][1000 genomes]
rs7548861	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552880	0.85[EUR][1000 genomes]
rs7552899	0.87[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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12129933	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
3	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
5	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
6	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
7	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
8	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:212967200-212989600	Weak transcription	NHLF	lung
11	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
13	chr1:212969600-212989000	Weak transcription	HepG2	liver
14	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:212970600-212985200	Weak transcription	Pancreas	Pancrea
16	chr1:212970600-212989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:212971000-212989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:212971400-212987600	Weak transcription	Small Intestine	intestine
20	chr1:212971400-212987800	Weak transcription	A549	lung
21	chr1:212971600-212988000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:212972000-212987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:212972400-212987800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:212972600-212988000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:212972600-212988000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:212972600-212988000	Weak transcription	Fetal Intestine Small	intestine
28	chr1:212972600-212989800	Weak transcription	HSMMtube	muscle
29	chr1:212972600-212990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:212973000-212988600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:212975600-212989600	Weak transcription	Brain Angular Gyrus	brain
32	chr1:212975800-212987200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
34	chr1:212976000-212989600	Weak transcription	HSMM	muscle
35	chr1:212976000-212989600	Weak transcription	K562	blood
36	chr1:212976000-212990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:212976000-212990200	Weak transcription	Fetal Brain Female	brain
38	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:212978200-212988000	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:212978200-212988400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:212978200-212989600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:212978200-212989800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:212978400-212989800	Weak transcription	Brain Germinal Matrix	brain
44	chr1:212979200-212994200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:212979400-212987800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:212979600-212987800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:212979600-212989800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:212979600-212992000	Weak transcription	Brain Anterior Caudate	brain
49	chr1:212979600-212993200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain

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