Variant report

Variant	rs35890547
Chromosome Location	chr2:171821118-171821119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1025242	0.80[EUR][1000 genomes]
rs1045327	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10515934	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803853	0.94[ASN][1000 genomes]
rs10803854	1.00[ASN][1000 genomes]
rs10930448	1.00[ASN][1000 genomes]
rs10930449	1.00[ASN][1000 genomes]
rs11553951	0.82[EUR][1000 genomes]
rs12151587	0.86[ASN][1000 genomes]
rs12471930	1.00[ASN][1000 genomes]
rs12612871	1.00[ASN][1000 genomes]
rs12988738	0.88[ASN][1000 genomes]
rs12996518	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997252	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12998296	0.83[EUR][1000 genomes]
rs13000644	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13000898	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13001088	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13002517	0.80[EUR][1000 genomes]
rs13003218	0.83[EUR][1000 genomes]
rs13006705	0.84[EUR][1000 genomes]
rs13007415	0.86[EUR][1000 genomes]
rs13011011	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015226	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13026444	0.82[EUR][1000 genomes]
rs13026662	0.94[ASN][1000 genomes]
rs13028857	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13035460	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1529391	1.00[ASN][1000 genomes]
rs16859066	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859081	0.91[ASN][1000 genomes]
rs17281735	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991370	0.83[EUR][1000 genomes]
rs2114738	0.94[ASN][1000 genomes]
rs2195116	0.86[ASN][1000 genomes]
rs2557799	0.94[ASN][1000 genomes]
rs34004615	0.91[ASN][1000 genomes]
rs34005022	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34017170	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34330182	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34342928	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34532258	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34563349	0.80[EUR][1000 genomes]
rs34911788	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35047553	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35123411	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230775	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35279794	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35332006	0.82[EUR][1000 genomes]
rs35381957	0.81[EUR][1000 genomes]
rs35864840	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35987434	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755125	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770435	0.86[ASN][1000 genomes]
rs3770440	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770441	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770442	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821090	0.87[EUR][1000 genomes]
rs4668349	0.89[ASN][1000 genomes]
rs4668350	0.89[ASN][1000 genomes]
rs4668355	1.00[ASN][1000 genomes]
rs55987132	0.80[EUR][1000 genomes]
rs56114146	0.83[EUR][1000 genomes]
rs6433267	0.94[ASN][1000 genomes]
rs6709077	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6714164	0.94[ASN][1000 genomes]
rs6714300	1.00[ASN][1000 genomes]
rs6715386	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724493	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6729847	0.94[ASN][1000 genomes]
rs6734903	0.91[ASN][1000 genomes]
rs6742797	1.00[ASN][1000 genomes]
rs6743201	0.91[ASN][1000 genomes]
rs6757510	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6758331	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71415229	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71415231	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415232	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415233	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72886381	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs731692	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731693	1.00[ASN][1000 genomes]
rs73976229	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570701	1.00[ASN][1000 genomes]
rs7587244	0.80[EUR][1000 genomes]
rs960222	0.86[ASN][1000 genomes]
rs965518	0.94[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
rs35890547	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	chr2:171803800-171824400	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:171803800-171825600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr2:171804000-171825000	Strong transcription	HepG2	liver
7	chr2:171804800-171824800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:171804800-171825800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:171805000-171824800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:171805000-171825000	Strong transcription	Dnd41	blood
11	chr2:171805200-171824800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:171805400-171824600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:171805400-171825000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:171805400-171825200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:171805400-171825400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:171805400-171825600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr2:171805400-171825800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:171805400-171825800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:171805600-171821800	Strong transcription	HSMM	muscle
20	chr2:171805600-171824600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:171805600-171824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:171805600-171825800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr2:171805800-171821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:171805800-171823800	Strong transcription	NHDF-Ad	bronchial
25	chr2:171805800-171825200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr2:171805800-171825800	Strong transcription	Placenta	Placenta
27	chr2:171805800-171825800	Strong transcription	Osteobl	bone
28	chr2:171805800-171826200	Strong transcription	Fetal Thymus	thymus
29	chr2:171806000-171821200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:171806000-171821600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:171806000-171821600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:171806000-171821800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:171806000-171821800	Strong transcription	NH-A	brain
34	chr2:171806000-171822200	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr2:171806000-171822400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:171806000-171823400	Strong transcription	Liver	Liver
37	chr2:171806000-171823800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:171806000-171824400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:171806000-171824400	Strong transcription	Left Ventricle	heart
40	chr2:171806000-171824800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:171806000-171825000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:171806000-171825000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:171806000-171825200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:171806000-171825200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:171806000-171825400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:171806000-171825800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr2:171806000-171826000	Strong transcription	Fetal Stomach	stomach
48	chr2:171806000-171826200	Strong transcription	Fetal Intestine Large	intestine
49	chr2:171806000-171826200	Strong transcription	Thymus	Thymus
50	chr2:171806000-171826800	Strong transcription	Fetal Muscle Leg	muscle

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