Variant report

Variant	rs6742564
Chromosome Location	chr2:171824432-171824433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171823033..171825275-chr2:171825625..171831472,9	K562	blood:
2	chr2:171824301..171825949-chr2:172284525..172287189,2	K562	blood:
3	chr2:171784385..171789962-chr2:171821380..171827816,10	K562	blood:
4	chr2:171821806..171826115-chr2:171826992..171831099,6	MCF-7	breast:
5	chr2:171824245..171828535-chr2:172013886..172017505,3	MCF-7	breast:
6	chr2:171823624..171825734-chr2:172290052..172291756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction
ENSG00000115806	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10803853	0.83[EUR][1000 genomes]
rs10803854	0.87[EUR][1000 genomes]
rs10930448	0.87[EUR][1000 genomes]
rs10930449	0.87[EUR][1000 genomes]
rs11686985	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11902360	0.81[ASN][1000 genomes]
rs11902369	0.81[ASN][1000 genomes]
rs12471930	0.88[EUR][1000 genomes]
rs12612871	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12618898	0.81[ASN][1000 genomes]
rs12621769	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13025033	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13026662	0.83[EUR][1000 genomes]
rs1529391	0.94[EUR][1000 genomes]
rs16859050	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2098999	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2114738	0.91[EUR][1000 genomes]
rs2356423	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3755124	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3755126	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3770438	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4667667	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4667673	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4668343	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4668344	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4668345	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4668346	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4668349	0.88[EUR][1000 genomes]
rs4668350	0.86[EUR][1000 genomes]
rs4668354	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668355	0.90[EUR][1000 genomes]
rs6433266	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6433267	0.84[EUR][1000 genomes]
rs6714300	0.88[EUR][1000 genomes]
rs6729847	0.84[EUR][1000 genomes]
rs6731774	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742797	0.88[EUR][1000 genomes]
rs6760293	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731693	0.88[EUR][1000 genomes]
rs754058	0.80[ASN][1000 genomes]
rs7559136	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7560889	0.82[ASN][1000 genomes]
rs7567927	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7570701	0.87[EUR][1000 genomes]
rs7585607	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7598194	0.83[ASN][1000 genomes]
rs965518	0.91[EUR][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
rs6742564	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
2	chr2:171797000-171830600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:171803600-171824600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:171803800-171825600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr2:171804000-171825000	Strong transcription	HepG2	liver
6	chr2:171804800-171824800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:171804800-171825800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:171805000-171824800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:171805000-171825000	Strong transcription	Dnd41	blood
10	chr2:171805200-171824800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:171805400-171824600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:171805400-171825000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:171805400-171825200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:171805400-171825400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:171805400-171825600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr2:171805400-171825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:171805400-171825800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:171805600-171824600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:171805600-171824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:171805600-171825800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr2:171805800-171825200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr2:171805800-171825800	Strong transcription	Placenta	Placenta
23	chr2:171805800-171825800	Strong transcription	Osteobl	bone
24	chr2:171805800-171826200	Strong transcription	Fetal Thymus	thymus
25	chr2:171806000-171824800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:171806000-171825000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:171806000-171825000	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:171806000-171825200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:171806000-171825200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:171806000-171825400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:171806000-171825800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:171806000-171826000	Strong transcription	Fetal Stomach	stomach
33	chr2:171806000-171826200	Strong transcription	Fetal Intestine Large	intestine
34	chr2:171806000-171826200	Strong transcription	Thymus	Thymus
35	chr2:171806000-171826800	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:171807600-171824800	Strong transcription	Primary B cells from cord blood	blood
37	chr2:171808200-171824600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:171808600-171825000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr2:171809200-171826200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:171811400-171830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr2:171814600-171829400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:171815600-171825800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:171815800-171825200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:171816400-171824600	Strong transcription	GM12878-XiMat	blood
45	chr2:171816800-171825800	Strong transcription	Primary T cells from cord blood	blood
46	chr2:171816800-171825800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:171817000-171825200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:171817200-171825000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:171817200-171825400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr2:171817200-171825600	Strong transcription	Brain Germinal Matrix	brain

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