Variant report

Variant	rs6742854
Chromosome Location	chr2:171928320-171928321
allele	A/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	chr2:171928004-171928444	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
TLK1	TF binding region

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10171850	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10182205	0.86[EUR][1000 genomes]
rs10183486	0.84[EUR][1000 genomes]
rs10186343	0.88[EUR][1000 genomes]
rs10198197	0.86[EUR][1000 genomes]
rs10208271	0.86[EUR][1000 genomes]
rs10208341	0.86[EUR][1000 genomes]
rs10210693	0.86[EUR][1000 genomes]
rs10210791	0.85[EUR][1000 genomes]
rs10210883	0.88[EUR][1000 genomes]
rs1025240	0.85[EUR][1000 genomes]
rs1025241	0.85[EUR][1000 genomes]
rs1035825	0.86[EUR][1000 genomes]
rs1035827	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1035828	0.92[EUR][1000 genomes]
rs10803855	0.86[EUR][1000 genomes]
rs10930453	0.86[EUR][1000 genomes]
rs10930455	0.86[EUR][1000 genomes]
rs10930456	0.86[EUR][1000 genomes]
rs10930457	0.86[EUR][1000 genomes]
rs11674590	0.85[EUR][1000 genomes]
rs11696064	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11899305	0.93[EUR][1000 genomes]
rs12053543	0.93[EUR][1000 genomes]
rs12477649	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614580	0.85[EUR][1000 genomes]
rs12618232	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12618898	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12624094	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004273	0.81[EUR][1000 genomes]
rs13010307	0.86[EUR][1000 genomes]
rs13025198	0.87[EUR][1000 genomes]
rs13030784	0.86[EUR][1000 genomes]
rs13034529	0.86[EUR][1000 genomes]
rs13036123	0.83[EUR][1000 genomes]
rs13395669	0.84[EUR][1000 genomes]
rs13401706	0.86[EUR][1000 genomes]
rs13402107	0.85[EUR][1000 genomes]
rs13403285	0.86[EUR][1000 genomes]
rs13410683	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13411575	0.86[EUR][1000 genomes]
rs13419444	0.86[EUR][1000 genomes]
rs13425247	0.86[EUR][1000 genomes]
rs13427723	0.86[EUR][1000 genomes]
rs13428613	0.86[EUR][1000 genomes]
rs13430489	0.86[EUR][1000 genomes]
rs13432813	0.86[EUR][1000 genomes]
rs1344237	0.85[EUR][1000 genomes]
rs1529378	0.86[EUR][1000 genomes]
rs16859081	0.80[EUR][1000 genomes]
rs16859142	0.86[EUR][1000 genomes]
rs17283147	0.92[EUR][1000 genomes]
rs1962841	0.93[EUR][1000 genomes]
rs1978592	0.83[EUR][1000 genomes]
rs2010114	0.93[EUR][1000 genomes]
rs2033160	0.93[EUR][1000 genomes]
rs2052808	0.93[EUR][1000 genomes]
rs2081715	0.86[EUR][1000 genomes]
rs2114595	0.93[EUR][1000 genomes]
rs2114596	0.85[EUR][1000 genomes]
rs2195117	0.84[EUR][1000 genomes]
rs2217154	0.86[EUR][1000 genomes]
rs2356423	0.83[EUR][1000 genomes]
rs2356593	0.94[EUR][1000 genomes]
rs2356597	0.94[EUR][1000 genomes]
rs2356599	0.84[EUR][1000 genomes]
rs2356608	0.85[EUR][1000 genomes]
rs2555922	0.92[EUR][1000 genomes]
rs2557794	0.81[EUR][1000 genomes]
rs2676131	0.92[EUR][1000 genomes]
rs2676151	0.82[EUR][1000 genomes]
rs2723233	0.94[EUR][1000 genomes]
rs34518725	0.87[EUR][1000 genomes]
rs34792013	0.94[EUR][1000 genomes]
rs35173138	0.86[EUR][1000 genomes]
rs35312173	0.84[EUR][1000 genomes]
rs35988467	0.84[EUR][1000 genomes]
rs36058634	0.94[EUR][1000 genomes]
rs3731990	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731991	0.93[EUR][1000 genomes]
rs3755121	0.86[EUR][1000 genomes]
rs3770423	0.86[EUR][1000 genomes]
rs3770428	0.84[EUR][1000 genomes]
rs3770435	0.81[EUR][1000 genomes]
rs4564745	0.86[EUR][1000 genomes]
rs4667673	0.81[EUR][1000 genomes]
rs4668368	0.94[EUR][1000 genomes]
rs5028603	0.93[EUR][1000 genomes]
rs55758155	0.86[EUR][1000 genomes]
rs55996750	0.83[EUR][1000 genomes]
rs56402728	0.86[EUR][1000 genomes]
rs56405950	0.85[EUR][1000 genomes]
rs6433276	0.82[EUR][1000 genomes]
rs6711287	0.94[EUR][1000 genomes]
rs6714164	0.80[EUR][1000 genomes]
rs6716127	0.85[EUR][1000 genomes]
rs6722537	0.85[EUR][1000 genomes]
rs6730417	0.85[EUR][1000 genomes]
rs6732229	0.87[EUR][1000 genomes]
rs6733178	0.87[EUR][1000 genomes]
rs6734542	0.85[EUR][1000 genomes]
rs6734903	0.80[EUR][1000 genomes]
rs6743201	0.80[EUR][1000 genomes]
rs6749427	0.84[EUR][1000 genomes]
rs6750849	0.85[EUR][1000 genomes]
rs6754315	0.86[EUR][1000 genomes]
rs6761596	0.87[EUR][1000 genomes]
rs6761642	0.86[EUR][1000 genomes]
rs7421377	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754058	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7578491	0.84[EUR][1000 genomes]
rs7580629	0.94[EUR][1000 genomes]
rs7581195	0.85[EUR][1000 genomes]
rs7581314	0.81[EUR][1000 genomes]
rs7585418	0.84[EUR][1000 genomes]
rs7593193	0.94[EUR][1000 genomes]
rs7600914	0.92[EUR][1000 genomes]
rs7603316	0.86[EUR][1000 genomes]
rs7603340	0.92[EUR][1000 genomes]
rs7603460	0.86[EUR][1000 genomes]
rs7606502	0.86[EUR][1000 genomes]
rs7606822	0.86[EUR][1000 genomes]
rs930035	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930036	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs958183	0.84[EUR][1000 genomes]
rs964172	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	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
rs6742854	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 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	chr2:171916400-171932200	Weak transcription	K562	blood
20	chr2:171916600-171930800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:171916600-171940000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:171916600-171944600	Weak transcription	Lung	lung
23	chr2:171916600-171950200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:171916600-171970800	Weak transcription	Ovary	ovary
25	chr2:171916800-171928800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:171916800-171935200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:171916800-171942200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:171916800-171943200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:171917000-171928400	Weak transcription	Thymus	Thymus
30	chr2:171917000-171928600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:171917000-171932000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:171917000-171934600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:171917000-171937200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:171917000-171940400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:171917000-171942600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:171917000-171942800	Weak transcription	Adipose Nuclei	Adipose
37	chr2:171917000-171942800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:171917000-171942800	Weak transcription	Gastric	stomach
39	chr2:171917000-171942800	Weak transcription	Left Ventricle	heart
40	chr2:171917000-171943000	Weak transcription	Osteobl	bone
41	chr2:171917000-171943200	Weak transcription	Fetal Lung	lung
42	chr2:171917000-171946200	Weak transcription	Psoas Muscle	Psoas
43	chr2:171917000-171948000	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:171917000-171953200	Weak transcription	HSMM	muscle
45	chr2:171917000-171956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:171917000-172000800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:171917200-171937600	Weak transcription	HUVEC	blood vessel
48	chr2:171917400-171943200	Weak transcription	NHDF-Ad	bronchial
49	chr2:171917600-171928400	Weak transcription	HepG2	liver
50	chr2:171917600-171928600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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