Variant report

Variant	rs34342928
Chromosome Location	chr2:171796101-171796102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:171788393..171792186-chr2:171793028..171799958,7	MCF-7	breast:
2	chr2:171784175..171787358-chr2:171794896..171797744,5	MCF-7	breast:
3	chr2:171783893..171791751-chr2:171794157..171800017,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1045327	0.84[EUR][1000 genomes]
rs10515934	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10803853	0.91[ASN][1000 genomes]
rs10803854	0.97[ASN][1000 genomes]
rs10930448	0.97[ASN][1000 genomes]
rs10930449	0.97[ASN][1000 genomes]
rs12151587	0.83[ASN][1000 genomes]
rs12471930	0.97[ASN][1000 genomes]
rs12612871	0.97[ASN][1000 genomes]
rs12988738	0.86[ASN][1000 genomes]
rs12996518	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12997252	0.81[EUR][1000 genomes]
rs13000644	0.84[EUR][1000 genomes]
rs13000898	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13001088	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13007415	0.81[EUR][1000 genomes]
rs13011011	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13015226	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13026662	0.91[ASN][1000 genomes]
rs13028857	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13035460	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1529391	0.97[ASN][1000 genomes]
rs16859066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16859081	0.88[ASN][1000 genomes]
rs17281735	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2114738	0.91[ASN][1000 genomes]
rs2195116	0.83[ASN][1000 genomes]
rs2557799	0.91[ASN][1000 genomes]
rs34004615	0.88[ASN][1000 genomes]
rs34005022	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34017170	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34330182	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34532258	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34911788	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35123411	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35230775	0.89[EUR][1000 genomes]
rs35279794	0.82[EUR][1000 genomes]
rs35864840	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35890547	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35987434	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755125	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770435	0.83[ASN][1000 genomes]
rs3770440	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770441	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770442	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3821090	0.93[EUR][1000 genomes]
rs4668349	0.86[ASN][1000 genomes]
rs4668350	0.86[ASN][1000 genomes]
rs4668355	0.97[ASN][1000 genomes]
rs6433267	0.91[ASN][1000 genomes]
rs6709077	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714164	0.91[ASN][1000 genomes]
rs6714300	0.97[ASN][1000 genomes]
rs6715386	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6724493	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6729847	0.91[ASN][1000 genomes]
rs6734903	0.88[ASN][1000 genomes]
rs6742797	0.97[ASN][1000 genomes]
rs6743201	0.88[ASN][1000 genomes]
rs6757510	0.81[EUR][1000 genomes]
rs6758331	0.83[EUR][1000 genomes]
rs71415229	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71415231	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71415232	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71415233	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72886381	0.81[EUR][1000 genomes]
rs731692	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs731693	0.97[ASN][1000 genomes]
rs73976229	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7570701	0.97[ASN][1000 genomes]
rs960222	0.83[ASN][1000 genomes]
rs965518	0.91[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
rs34342928	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787000-171810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:171787400-171806000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:171787400-171806000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:171787400-171806000	Weak transcription	Esophagus	oesophagus
5	chr2:171787400-171806000	Weak transcription	Psoas Muscle	Psoas
6	chr2:171787400-171807200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:171787400-171808200	Weak transcription	Aorta	Aorta
8	chr2:171787400-171810000	Weak transcription	Small Intestine	intestine
9	chr2:171787600-171796600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:171787600-171806800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:171787600-171807600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
13	chr2:171787800-171798800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:171787800-171806000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:171787800-171806000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:171787800-171806200	Weak transcription	Fetal Kidney	kidney
17	chr2:171787800-171806600	Weak transcription	Fetal Brain Female	brain
18	chr2:171787800-171807000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:171787800-171807400	Weak transcription	Brain Germinal Matrix	brain
20	chr2:171787800-171809200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:171788000-171805800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:171788000-171806000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:171788000-171806000	Weak transcription	Brain Substantia Nigra	brain
24	chr2:171788000-171806200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:171788000-171806600	Weak transcription	Fetal Lung	lung
26	chr2:171788000-171806800	Weak transcription	Brain Anterior Caudate	brain
27	chr2:171788000-171806800	Weak transcription	A549	lung
28	chr2:171788000-171807600	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:171788000-171808400	Weak transcription	Brain Angular Gyrus	brain
30	chr2:171788200-171806200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:171788400-171805400	Weak transcription	HUVEC	blood vessel
32	chr2:171788400-171805600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:171788400-171806200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:171789000-171805600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:171789400-171798800	Weak transcription	NHDF-Ad	bronchial
36	chr2:171789400-171805400	Weak transcription	Hela-S3	cervix
37	chr2:171789400-171805800	Weak transcription	Osteobl	bone
38	chr2:171789400-171806000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:171789600-171810000	Weak transcription	Stomach Mucosa	stomach
40	chr2:171790600-171806000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:171791200-171799000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:171791600-171806000	Weak transcription	Lung	lung
43	chr2:171791800-171797000	Strong transcription	Fetal Intestine Large	intestine
44	chr2:171792400-171806000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:171793400-171803600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:171793400-171806000	Weak transcription	Thymus	Thymus
47	chr2:171793400-171806000	Weak transcription	NH-A	brain
48	chr2:171793600-171796400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:171793800-171797200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:171794000-171802600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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