Variant report

Variant	rs3731990
Chromosome Location	chr2:171916371-171916372
allele	A/G
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	chr2:171916310-171916438	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171906152..171909265-chr2:171915345..171919529,4	K562	blood:

Variant related genes	Relation type
TLK1	TF binding region

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10171850	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10182205	0.85[EUR][1000 genomes]
rs10183486	0.82[EUR][1000 genomes]
rs10186343	0.86[EUR][1000 genomes]
rs10198197	0.84[EUR][1000 genomes]
rs10208271	0.84[EUR][1000 genomes]
rs10208341	0.84[EUR][1000 genomes]
rs10210693	0.84[EUR][1000 genomes]
rs10210791	0.84[EUR][1000 genomes]
rs10210883	0.86[EUR][1000 genomes]
rs1025240	0.84[EUR][1000 genomes]
rs1025241	0.84[EUR][1000 genomes]
rs1035825	0.85[EUR][1000 genomes]
rs1035827	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1035828	0.93[EUR][1000 genomes]
rs10803855	0.88[EUR][1000 genomes]
rs10930453	0.88[EUR][1000 genomes]
rs10930455	0.85[EUR][1000 genomes]
rs10930456	0.85[EUR][1000 genomes]
rs10930457	0.85[EUR][1000 genomes]
rs11674590	0.87[EUR][1000 genomes]
rs11696064	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11899305	0.94[EUR][1000 genomes]
rs12053543	0.92[EUR][1000 genomes]
rs12477649	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614580	0.86[EUR][1000 genomes]
rs12618232	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618898	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12624094	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12988738	0.81[EUR][1000 genomes]
rs13004273	0.83[EUR][1000 genomes]
rs13010307	0.84[EUR][1000 genomes]
rs13025198	0.85[EUR][1000 genomes]
rs13030784	0.84[EUR][1000 genomes]
rs13034529	0.85[EUR][1000 genomes]
rs13036123	0.81[EUR][1000 genomes]
rs13395669	0.83[EUR][1000 genomes]
rs13401706	0.84[EUR][1000 genomes]
rs13402107	0.84[EUR][1000 genomes]
rs13403285	0.84[EUR][1000 genomes]
rs13410683	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13411575	0.85[EUR][1000 genomes]
rs13419444	0.85[EUR][1000 genomes]
rs13425247	0.85[EUR][1000 genomes]
rs13427723	0.84[EUR][1000 genomes]
rs13428613	0.84[EUR][1000 genomes]
rs13430489	0.84[EUR][1000 genomes]
rs13432813	0.84[EUR][1000 genomes]
rs1344237	0.84[EUR][1000 genomes]
rs1529378	0.85[EUR][1000 genomes]
rs16859081	0.82[EUR][1000 genomes]
rs16859142	0.85[EUR][1000 genomes]
rs17283147	0.94[EUR][1000 genomes]
rs1962841	0.92[EUR][1000 genomes]
rs1978592	0.84[EUR][1000 genomes]
rs2010114	0.92[EUR][1000 genomes]
rs2033160	0.94[EUR][1000 genomes]
rs2052808	0.94[EUR][1000 genomes]
rs2059724	0.81[EUR][1000 genomes]
rs2081715	0.84[EUR][1000 genomes]
rs2114595	0.94[EUR][1000 genomes]
rs2114596	0.83[EUR][1000 genomes]
rs2195117	0.85[EUR][1000 genomes]
rs2217154	0.84[EUR][1000 genomes]
rs2356423	0.84[EUR][1000 genomes]
rs2356593	0.92[EUR][1000 genomes]
rs2356597	0.93[EUR][1000 genomes]
rs2356599	0.83[EUR][1000 genomes]
rs2356608	0.84[EUR][1000 genomes]
rs2555922	0.94[EUR][1000 genomes]
rs2557794	0.83[EUR][1000 genomes]
rs2557799	0.81[EUR][1000 genomes]
rs2676131	0.94[EUR][1000 genomes]
rs2676151	0.84[EUR][1000 genomes]
rs2723233	0.92[EUR][1000 genomes]
rs34004615	0.81[EUR][1000 genomes]
rs34518725	0.85[EUR][1000 genomes]
rs34792013	0.93[EUR][1000 genomes]
rs35173138	0.85[EUR][1000 genomes]
rs35312173	0.82[EUR][1000 genomes]
rs35988467	0.83[EUR][1000 genomes]
rs36058634	0.92[EUR][1000 genomes]
rs3731991	0.94[EUR][1000 genomes]
rs3755121	0.85[EUR][1000 genomes]
rs3770423	0.85[EUR][1000 genomes]
rs3770428	0.85[EUR][1000 genomes]
rs3770435	0.83[EUR][1000 genomes]
rs4564745	0.84[EUR][1000 genomes]
rs4667673	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4668368	0.93[EUR][1000 genomes]
rs5028603	0.94[EUR][1000 genomes]
rs55758155	0.84[EUR][1000 genomes]
rs55996750	0.85[EUR][1000 genomes]
rs56402728	0.84[EUR][1000 genomes]
rs56405950	0.84[EUR][1000 genomes]
rs6433276	0.83[EUR][1000 genomes]
rs6711287	0.93[EUR][1000 genomes]
rs6714164	0.82[EUR][1000 genomes]
rs6715332	0.81[EUR][1000 genomes]
rs6716127	0.83[EUR][1000 genomes]
rs6722537	0.87[EUR][1000 genomes]
rs6730417	0.84[EUR][1000 genomes]
rs6732229	0.85[EUR][1000 genomes]
rs6733178	0.85[EUR][1000 genomes]
rs6734542	0.87[EUR][1000 genomes]
rs6734903	0.82[EUR][1000 genomes]
rs6742854	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6743201	0.82[EUR][1000 genomes]
rs6749427	0.83[EUR][1000 genomes]
rs6750849	0.87[EUR][1000 genomes]
rs6754315	0.85[EUR][1000 genomes]
rs6761596	0.85[EUR][1000 genomes]
rs6761642	0.84[EUR][1000 genomes]
rs7421377	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754058	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7578491	0.82[EUR][1000 genomes]
rs7580629	0.93[EUR][1000 genomes]
rs7581195	0.83[EUR][1000 genomes]
rs7585418	0.86[EUR][1000 genomes]
rs7593193	0.92[EUR][1000 genomes]
rs7600914	0.94[EUR][1000 genomes]
rs7603316	0.84[EUR][1000 genomes]
rs7603340	0.94[EUR][1000 genomes]
rs7603460	0.85[EUR][1000 genomes]
rs7606502	0.85[EUR][1000 genomes]
rs7606822	0.84[EUR][1000 genomes]
rs930035	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930036	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs958183	0.82[EUR][1000 genomes]
rs960222	0.80[EUR][1000 genomes]
rs964172	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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
rs3731990	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr2:171862600-171918400	Weak transcription	Brain Germinal Matrix	brain
3	chr2:171862800-171931200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:171878000-171943200	Weak transcription	Small Intestine	intestine
5	chr2:171878800-171940000	Weak transcription	Stomach Mucosa	stomach
6	chr2:171890400-171917600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:171892400-171943400	Weak transcription	Spleen	Spleen
8	chr2:171892600-171918200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:171892800-171918000	Weak transcription	NHLF	lung
10	chr2:171893200-171918400	Weak transcription	Fetal Brain Female	brain
11	chr2:171895000-171918000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:171895400-171917600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:171895800-171918000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:171897200-171917600	Strong transcription	Primary B cells from cord blood	blood
15	chr2:171898200-171916400	Weak transcription	Lung	lung
16	chr2:171898200-171928800	Weak transcription	Fetal Stomach	stomach
17	chr2:171898200-171946200	Weak transcription	Pancreas	Pancrea
18	chr2:171900000-171940000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:171900200-171918400	Strong transcription	Dnd41	blood
20	chr2:171900200-171936400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:171900200-171937800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:171900400-171975400	Weak transcription	Aorta	Aorta
23	chr2:171902000-171918000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:171902000-171924200	Weak transcription	Fetal Intestine Small	intestine
25	chr2:171902400-171918200	Weak transcription	Colonic Mucosa	Colon
26	chr2:171903000-171940000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr2:171903400-171916800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:171904000-171921000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:171904800-171917600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:171904800-171917800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:171904800-171918200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:171905000-171917800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:171905600-171921200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:171905800-171918400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:171905800-171939200	Weak transcription	HSMMtube	muscle
36	chr2:171906000-171918400	Weak transcription	Fetal Heart	heart
37	chr2:171907800-171942800	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:171908000-171917400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:171908000-171917600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:171908200-171928400	Weak transcription	Fetal Kidney	kidney
41	chr2:171908200-171932200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:171909200-171917600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:171910200-171916400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:171910200-171916800	Strong transcription	A549	lung
45	chr2:171910200-171920600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:171910600-171917000	Strong transcription	HSMM	muscle
47	chr2:171910600-171919600	Strong transcription	GM12878-XiMat	blood
48	chr2:171911600-171943200	Weak transcription	NH-A	brain
49	chr2:171912200-171917000	Strong transcription	Primary T cells from cord blood	blood
50	chr2:171912400-171916400	Strong transcription	K562	blood

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