Variant report

Variant	rs12053543
Chromosome Location	chr2:171924753-171924754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:171924706-171924784	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171920035..171922996-chr2:171924584..171926973,3	K562	blood:

Variant related genes	Relation type
TLK1	TF binding region

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10177560	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10182205	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10183486	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10186343	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10191270	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10198197	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10199500	0.81[EUR][1000 genomes]
rs10208271	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10208341	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10210693	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10210791	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10210883	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1025240	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1025241	0.89[EUR][1000 genomes]
rs1035825	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1035827	0.89[EUR][1000 genomes]
rs1035828	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10803855	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930453	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930455	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10930456	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10930457	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11674590	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11696064	0.91[EUR][1000 genomes]
rs11899305	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12477649	0.85[EUR][1000 genomes]
rs12614580	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12618232	0.91[EUR][1000 genomes]
rs12624094	0.80[EUR][1000 genomes]
rs12988738	0.82[EUR][1000 genomes]
rs12997252	0.86[ASN][1000 genomes]
rs12998296	0.86[ASN][1000 genomes]
rs13004273	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13010307	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025198	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13030784	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13034529	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13036123	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13395669	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13401706	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13402107	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13403285	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13410683	0.85[EUR][1000 genomes]
rs13411575	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13419444	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13425247	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13427723	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13428613	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13430489	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13432813	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1344237	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1529378	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859081	0.83[EUR][1000 genomes]
rs16859142	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17283147	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1962841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1978592	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1991370	0.86[ASN][1000 genomes]
rs2010114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2033160	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2052808	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2059724	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2081715	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2114595	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2114596	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2195117	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2217154	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2356593	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2356597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2356599	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2356608	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2555922	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2557794	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2557799	0.82[EUR][1000 genomes]
rs2676131	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2676151	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2723233	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2723241	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34004615	0.82[EUR][1000 genomes]
rs34518725	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34792013	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35173138	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35312173	0.88[EUR][1000 genomes]
rs35900609	0.86[ASN][1000 genomes]
rs35988467	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36058634	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3731990	0.92[EUR][1000 genomes]
rs3731991	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755121	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3770423	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770428	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770433	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770435	0.84[EUR][1000 genomes]
rs4564745	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4668368	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5028603	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55758155	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55996750	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56114146	0.86[ASN][1000 genomes]
rs56402728	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56405950	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6433276	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6710714	0.84[AMR][1000 genomes]
rs6711287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6714164	0.83[EUR][1000 genomes]
rs6715332	0.82[EUR][1000 genomes]
rs6716127	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6719647	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6722537	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6730417	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732229	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6733178	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6734542	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734903	0.83[EUR][1000 genomes]
rs6742854	0.93[EUR][1000 genomes]
rs6743201	0.83[EUR][1000 genomes]
rs6749427	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750849	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6754315	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6761596	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6761642	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71415235	0.86[ASN][1000 genomes]
rs7421377	0.85[EUR][1000 genomes]
rs7578491	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7580629	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7581195	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7581314	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7585418	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7593193	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7597940	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7600914	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7603316	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7603340	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7603460	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606502	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7606822	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs930035	0.86[EUR][1000 genomes]
rs930036	0.86[EUR][1000 genomes]
rs958183	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs960222	0.81[EUR][1000 genomes]
rs964172	0.86[EUR][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	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv834456	chr2:171874210-172014659	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12053543	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171841600-171940000	Weak transcription	Right Ventricle	heart
2	chr2:171862800-171931200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:171878000-171943200	Weak transcription	Small Intestine	intestine
4	chr2:171878800-171940000	Weak transcription	Stomach Mucosa	stomach
5	chr2:171892400-171943400	Weak transcription	Spleen	Spleen
6	chr2:171898200-171928800	Weak transcription	Fetal Stomach	stomach
7	chr2:171898200-171946200	Weak transcription	Pancreas	Pancrea
8	chr2:171900000-171940000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:171900200-171936400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:171900200-171937800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:171900400-171975400	Weak transcription	Aorta	Aorta
12	chr2:171903000-171940000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:171905800-171939200	Weak transcription	HSMMtube	muscle
14	chr2:171907800-171942800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:171908200-171928400	Weak transcription	Fetal Kidney	kidney
16	chr2:171908200-171932200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:171911600-171943200	Weak transcription	NH-A	brain
18	chr2:171912400-171937400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:171914200-171925800	Weak transcription	HMEC	breast
20	chr2:171916400-171932200	Weak transcription	K562	blood
21	chr2:171916600-171928000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:171916600-171930800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:171916600-171940000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:171916600-171944600	Weak transcription	Lung	lung
25	chr2:171916600-171950200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:171916600-171970800	Weak transcription	Ovary	ovary
27	chr2:171916800-171925600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:171916800-171926000	Weak transcription	A549	lung
29	chr2:171916800-171928800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:171916800-171935200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:171916800-171942200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:171916800-171943200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:171917000-171925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:171917000-171925800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:171917000-171926000	Weak transcription	NHEK	skin
36	chr2:171917000-171927000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:171917000-171927400	Weak transcription	Primary T cells from cord blood	blood
38	chr2:171917000-171928400	Weak transcription	Thymus	Thymus
39	chr2:171917000-171928600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:171917000-171932000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:171917000-171934600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:171917000-171937200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:171917000-171940400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:171917000-171942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:171917000-171942800	Weak transcription	Adipose Nuclei	Adipose
46	chr2:171917000-171942800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:171917000-171942800	Weak transcription	Gastric	stomach
48	chr2:171917000-171942800	Weak transcription	Left Ventricle	heart
49	chr2:171917000-171943000	Weak transcription	Osteobl	bone
50	chr2:171917000-171943200	Weak transcription	Fetal Lung	lung

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