Variant report

Variant	rs12996518
Chromosome Location	chr2:171793568-171793569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171788393..171792186-chr2:171793028..171799958,7	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1045327	0.84[EUR][1000 genomes]
rs10515934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
rs12151587	0.86[ASN][1000 genomes]
rs12471930	1.00[ASN][1000 genomes]
rs12612871	1.00[ASN][1000 genomes]
rs12988738	0.88[ASN][1000 genomes]
rs12997252	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13000644	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13000898	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13001088	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13007415	0.81[EUR][1000 genomes]
rs13011011	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015226	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13026662	0.94[ASN][1000 genomes]
rs13028857	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13035460	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1529391	1.00[ASN][1000 genomes]
rs16859066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859081	0.91[ASN][1000 genomes]
rs17281735	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34017170	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34330182	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34342928	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34532258	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34911788	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34960296	0.82[AMR][1000 genomes]
rs35123411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35230775	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35279794	0.82[EUR][1000 genomes]
rs35864840	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35890547	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35900609	0.80[AMR][1000 genomes]
rs35987434	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755125	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770435	0.86[ASN][1000 genomes]
rs3770440	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770441	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770442	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821090	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4668349	0.89[ASN][1000 genomes]
rs4668350	0.89[ASN][1000 genomes]
rs4668355	1.00[ASN][1000 genomes]
rs6433267	0.94[ASN][1000 genomes]
rs6709077	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6714164	0.94[ASN][1000 genomes]
rs6714300	1.00[ASN][1000 genomes]
rs6715386	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724493	0.90[AMR][1000 genomes];0.89[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[EUR][1000 genomes]
rs6758331	0.83[EUR][1000 genomes]
rs71415229	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71415231	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415233	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415235	0.80[AMR][1000 genomes]
rs72886381	0.81[EUR][1000 genomes]
rs731692	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731693	1.00[ASN][1000 genomes]
rs73976229	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570701	1.00[ASN][1000 genomes]
rs7593186	0.82[AMR][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
rs12996518	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	chr2:171787000-171793800	Weak transcription	Gastric	stomach
2	chr2:171787000-171810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:171787200-171793800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:171787200-171795200	Weak transcription	Ovary	ovary
5	chr2:171787400-171806000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:171787400-171806000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:171787400-171806000	Weak transcription	Esophagus	oesophagus
8	chr2:171787400-171806000	Weak transcription	Psoas Muscle	Psoas
9	chr2:171787400-171807200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:171787400-171808200	Weak transcription	Aorta	Aorta
11	chr2:171787400-171810000	Weak transcription	Small Intestine	intestine
12	chr2:171787600-171793800	Weak transcription	Right Ventricle	heart
13	chr2:171787600-171796600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:171787600-171806800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:171787600-171807600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
17	chr2:171787800-171795000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:171787800-171795800	Weak transcription	Primary B cells from cord blood	blood
19	chr2:171787800-171798800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:171787800-171806000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:171787800-171806000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:171787800-171806200	Weak transcription	Fetal Kidney	kidney
23	chr2:171787800-171806600	Weak transcription	Fetal Brain Female	brain
24	chr2:171787800-171807000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:171787800-171807400	Weak transcription	Brain Germinal Matrix	brain
26	chr2:171787800-171809200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:171788000-171794200	Weak transcription	HMEC	breast
28	chr2:171788000-171794400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:171788000-171805800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:171788000-171806000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:171788000-171806000	Weak transcription	Brain Substantia Nigra	brain
32	chr2:171788000-171806200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:171788000-171806600	Weak transcription	Fetal Lung	lung
34	chr2:171788000-171806800	Weak transcription	Brain Anterior Caudate	brain
35	chr2:171788000-171806800	Weak transcription	A549	lung
36	chr2:171788000-171807600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:171788000-171808400	Weak transcription	Brain Angular Gyrus	brain
38	chr2:171788200-171795600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:171788200-171806200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:171788400-171805400	Weak transcription	HUVEC	blood vessel
41	chr2:171788400-171805600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:171788400-171806200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:171788800-171795400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:171789000-171793600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:171789000-171794400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:171789000-171795800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:171789000-171805600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:171789200-171795200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:171789400-171794400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:171789400-171798800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links