Variant report

Variant	rs2557799
Chromosome Location	chr2:171840249-171840250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171839559..171842125-chr2:171855195..171857476,2	K562	blood:
2	chr2:171839549..171841801-chr2:171844212..171847084,2	K562	blood:
3	chr2:171840049..171842807-chr2:171844116..171846673,2	MCF-7	breast:
4	chr2:171831373..171832895-chr2:171839356..171842294,2	K562	blood:
5	chr2:171839960..171842207-chr2:171852236..171854896,2	K562	blood:

Extended variants
information (count: 183 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:182)

rs_ID	r²[population]
rs10182205	0.89[EUR][1000 genomes]
rs10183486	0.86[EUR][1000 genomes]
rs10186343	0.90[EUR][1000 genomes]
rs10191270	0.80[EUR][1000 genomes]
rs10198197	0.88[EUR][1000 genomes]
rs10208271	0.88[EUR][1000 genomes]
rs10208341	0.88[EUR][1000 genomes]
rs10210693	0.88[EUR][1000 genomes]
rs10210791	0.87[EUR][1000 genomes]
rs10210883	0.90[EUR][1000 genomes]
rs1025240	0.87[EUR][1000 genomes]
rs1025241	0.88[EUR][1000 genomes]
rs1035825	0.89[EUR][1000 genomes]
rs1035828	0.83[EUR][1000 genomes]
rs10515934	0.94[ASN][1000 genomes]
rs10803853	0.88[ASN][1000 genomes]
rs10803854	0.94[ASN][1000 genomes]
rs10803855	0.91[EUR][1000 genomes]
rs10930448	0.94[ASN][1000 genomes]
rs10930449	0.94[ASN][1000 genomes]
rs10930453	0.91[EUR][1000 genomes]
rs10930455	0.89[EUR][1000 genomes]
rs10930456	0.89[EUR][1000 genomes]
rs10930457	0.89[EUR][1000 genomes]
rs11674590	0.91[EUR][1000 genomes]
rs11899305	0.84[EUR][1000 genomes]
rs12053543	0.82[EUR][1000 genomes]
rs12151587	0.92[ASN][1000 genomes]
rs12471930	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12477649	0.84[EUR][1000 genomes]
rs12612871	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614580	0.90[EUR][1000 genomes]
rs12624094	0.83[EUR][1000 genomes]
rs12988738	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12996518	0.94[ASN][1000 genomes]
rs13000644	0.82[ASN][1000 genomes]
rs13000898	0.97[ASN][1000 genomes]
rs13004273	0.95[EUR][1000 genomes]
rs13010307	0.88[EUR][1000 genomes]
rs13011011	0.82[ASN][1000 genomes]
rs13015226	0.88[ASN][1000 genomes]
rs13025198	0.89[EUR][1000 genomes]
rs13026662	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028857	0.88[ASN][1000 genomes]
rs13030784	0.88[EUR][1000 genomes]
rs13034529	0.89[EUR][1000 genomes]
rs13035460	0.88[ASN][1000 genomes]
rs13036123	0.85[EUR][1000 genomes]
rs13395669	0.86[EUR][1000 genomes]
rs13401706	0.88[EUR][1000 genomes]
rs13402107	0.87[EUR][1000 genomes]
rs13403285	0.88[EUR][1000 genomes]
rs13410683	0.84[EUR][1000 genomes]
rs13411575	0.89[EUR][1000 genomes]
rs13419444	0.89[EUR][1000 genomes]
rs13425247	0.89[EUR][1000 genomes]
rs13427723	0.88[EUR][1000 genomes]
rs13428613	0.88[EUR][1000 genomes]
rs13430489	0.88[EUR][1000 genomes]
rs13432813	0.88[EUR][1000 genomes]
rs1344237	0.87[EUR][1000 genomes]
rs1529378	0.89[EUR][1000 genomes]
rs1529391	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859066	0.94[ASN][1000 genomes]
rs16859081	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16859142	0.90[EUR][1000 genomes]
rs17281735	0.94[ASN][1000 genomes]
rs17283147	0.84[EUR][1000 genomes]
rs1962841	0.82[EUR][1000 genomes]
rs1978592	0.91[EUR][1000 genomes]
rs2010114	0.82[EUR][1000 genomes]
rs2033160	0.84[EUR][1000 genomes]
rs2052808	0.84[EUR][1000 genomes]
rs2059724	0.92[EUR][1000 genomes]
rs2081715	0.88[EUR][1000 genomes]
rs2114595	0.84[EUR][1000 genomes]
rs2114596	0.87[EUR][1000 genomes]
rs2114738	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195116	0.80[ASN][1000 genomes]
rs2195117	0.92[EUR][1000 genomes]
rs2217154	0.88[EUR][1000 genomes]
rs2356423	0.85[EUR][1000 genomes]
rs2356593	0.82[EUR][1000 genomes]
rs2356597	0.83[EUR][1000 genomes]
rs2356599	0.86[EUR][1000 genomes]
rs2356608	0.87[EUR][1000 genomes]
rs2555922	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2557794	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2676131	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2676151	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2723233	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2723241	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs34004615	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34005022	0.88[ASN][1000 genomes]
rs34017170	0.85[ASN][1000 genomes]
rs34330182	0.82[ASN][1000 genomes]
rs34342928	0.91[ASN][1000 genomes]
rs34518725	0.90[EUR][1000 genomes]
rs34792013	0.83[EUR][1000 genomes]
rs34911788	0.88[ASN][1000 genomes]
rs35123411	0.94[ASN][1000 genomes]
rs35173138	0.89[EUR][1000 genomes]
rs35312173	0.87[EUR][1000 genomes]
rs35864840	0.85[ASN][1000 genomes]
rs35890547	0.94[ASN][1000 genomes]
rs35987434	1.00[ASN][1000 genomes]
rs35988467	0.86[EUR][1000 genomes]
rs36058634	0.83[EUR][1000 genomes]
rs3731990	0.81[EUR][1000 genomes]
rs3731991	0.84[EUR][1000 genomes]
rs3755121	0.89[EUR][1000 genomes]
rs3755125	0.88[ASN][1000 genomes]
rs3770423	0.90[EUR][1000 genomes]
rs3770428	0.92[EUR][1000 genomes]
rs3770433	0.88[EUR][1000 genomes]
rs3770435	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3770440	0.94[ASN][1000 genomes]
rs3770441	0.88[ASN][1000 genomes]
rs4544401	0.89[EUR][1000 genomes]
rs4564745	0.88[EUR][1000 genomes]
rs4667673	0.88[EUR][1000 genomes]
rs4668349	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668350	0.84[ASN][1000 genomes]
rs4668355	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668368	0.83[EUR][1000 genomes]
rs5028603	0.84[EUR][1000 genomes]
rs55758155	0.88[EUR][1000 genomes]
rs55996750	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56402728	0.88[EUR][1000 genomes]
rs56405950	0.87[EUR][1000 genomes]
rs6433267	0.88[ASN][1000 genomes]
rs6433276	0.95[EUR][1000 genomes]
rs6709077	0.85[ASN][1000 genomes]
rs6711287	0.83[EUR][1000 genomes]
rs6714164	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714300	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715332	0.93[EUR][1000 genomes]
rs6715386	0.88[ASN][1000 genomes]
rs6716127	0.87[EUR][1000 genomes]
rs6722537	0.92[EUR][1000 genomes]
rs6724493	0.88[ASN][1000 genomes]
rs6729847	0.88[ASN][1000 genomes]
rs6730417	0.87[EUR][1000 genomes]
rs6732229	0.89[EUR][1000 genomes]
rs6733178	0.89[EUR][1000 genomes]
rs6734542	0.92[EUR][1000 genomes]
rs6734903	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6742797	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743201	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6749427	0.86[EUR][1000 genomes]
rs6750849	0.92[EUR][1000 genomes]
rs6754315	0.89[EUR][1000 genomes]
rs6761596	0.89[EUR][1000 genomes]
rs6761642	0.88[EUR][1000 genomes]
rs71415229	0.88[ASN][1000 genomes]
rs71415231	0.82[ASN][1000 genomes]
rs71415232	0.94[ASN][1000 genomes]
rs71415233	0.82[ASN][1000 genomes]
rs731692	0.82[ASN][1000 genomes]
rs731693	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73976229	0.94[ASN][1000 genomes]
rs7421377	0.84[EUR][1000 genomes]
rs7570701	0.94[ASN][1000 genomes]
rs7578491	0.86[EUR][1000 genomes]
rs7580629	0.83[EUR][1000 genomes]
rs7581195	0.87[EUR][1000 genomes]
rs7581314	0.83[EUR][1000 genomes]
rs7585418	0.93[EUR][1000 genomes]
rs7593193	0.82[EUR][1000 genomes]
rs7597940	0.81[EUR][1000 genomes]
rs7600914	0.85[EUR][1000 genomes]
rs7603316	0.88[EUR][1000 genomes]
rs7603340	0.85[EUR][1000 genomes]
rs7603460	0.89[EUR][1000 genomes]
rs7606502	0.89[EUR][1000 genomes]
rs7606822	0.90[EUR][1000 genomes]
rs930035	0.85[EUR][1000 genomes]
rs930036	0.85[EUR][1000 genomes]
rs958183	0.87[EUR][1000 genomes]
rs960222	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs964172	0.85[EUR][1000 genomes]
rs965518	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2557799	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171830400-171842200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:171830600-171902800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:171830800-171891400	Weak transcription	Spleen	Spleen
4	chr2:171831000-171847600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:171831000-171850000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:171831200-171840400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:171831200-171843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:171831200-171845400	Weak transcription	HMEC	breast
9	chr2:171831200-171845800	Weak transcription	Osteobl	bone
10	chr2:171831200-171847000	Weak transcription	A549	lung
11	chr2:171831200-171857400	Weak transcription	HSMMtube	muscle
12	chr2:171831400-171849400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:171831400-171857000	Weak transcription	NHEK	skin
14	chr2:171831400-171879200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:171831400-171916200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:171832000-171844800	Weak transcription	GM12878-XiMat	blood
17	chr2:171832600-171846000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:171832600-171852200	Weak transcription	Fetal Intestine Small	intestine
19	chr2:171833000-171848800	Weak transcription	HepG2	liver
20	chr2:171835600-171843400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:171836600-171844800	Weak transcription	Primary T cells from cord blood	blood
22	chr2:171837600-171849200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:171838400-171849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:171838600-171862000	Weak transcription	Ovary	ovary
25	chr2:171838800-171843800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:171838800-171845400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:171838800-171847600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:171838800-171861800	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:171839000-171852400	Weak transcription	NHLF	lung
30	chr2:171839200-171843400	Weak transcription	Placenta	Placenta
31	chr2:171839200-171846600	Weak transcription	Liver	Liver
32	chr2:171839200-171847200	Weak transcription	K562	blood
33	chr2:171839200-171854800	Weak transcription	Pancreas	Pancrea
34	chr2:171839400-171844600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:171839600-171844600	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:171839800-171840600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:171839800-171840800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:171839800-171841200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr2:171839800-171843200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:171839800-171843200	Weak transcription	HSMM	muscle
41	chr2:171839800-171845600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:171840000-171841000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:171840000-171841000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr2:171840000-171841000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr2:171840000-171841000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr2:171840000-171841000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:171840000-171841000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:171840200-171845000	Weak transcription	Primary B cells from cord blood	blood

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