Variant report

Variant	rs13429113
Chromosome Location	chr2:172552765-172552766
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172550811..172553362-chr2:172778656..172780423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128708	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10166005	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10167419	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10174525	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10184866	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10194102	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10200608	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10201419	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10204502	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10204622	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10206062	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10207085	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497374	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10803863	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1113389	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11678984	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11757	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11886820	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11897196	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11904009	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12053003	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12185567	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12692970	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12692973	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12692974	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12692978	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13017585	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13018768	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13022113	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13419987	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13429409	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474074	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1554166	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1973706	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292815	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357061	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2674484	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2678155	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs312916	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs312918	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs312919	0.93[AMR][1000 genomes]
rs312921	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs312924	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312925	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34358700	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34542126	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35379278	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35391289	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35549875	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35854280	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36057702	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770445	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770451	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770452	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3795999	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667693	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667694	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4668407	0.82[EUR][1000 genomes]
rs4668412	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4668414	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6433311	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433314	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66835971	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6705200	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6709156	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710698	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67204065	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6721680	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722757	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6724337	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6725388	0.80[AMR][1000 genomes]
rs6738445	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6745143	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6754817	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6757773	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6758704	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6759575	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71013062	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7355523	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7355594	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562356	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7572215	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7573003	0.82[AMR][1000 genomes]
rs7586207	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7597387	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7604918	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7608403	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs908670	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs908671	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs973889	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13429113	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs13429113	AC068039.4	cis	Whole Blood	GTEx
rs13429113	AC068039.4	cis	Nerve Tibial	GTEx
rs13429113	AC068039.4	cis	Stomach	GTEx
rs13429113	AC068039.4	cis	Muscle Skeletal	GTEx
rs13429113	AC068039.4	cis	Heart Left Ventricle	GTEx
rs13429113	AC068039.4	cis	Esophagus Mucosa	GTEx
rs13429113	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs13429113	AC068039.4	cis	Esophagus Muscularis	GTEx
rs13429113	AC068039.4	cis	lung	GTEx
rs13429113	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs13429113	AC068039.4	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172553600	Weak transcription	Esophagus	oesophagus
2	chr2:172545000-172553600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
4	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
5	chr2:172545000-172580800	Weak transcription	Gastric	stomach
6	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:172545800-172553600	Weak transcription	Aorta	Aorta
9	chr2:172545800-172553800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:172545800-172556600	Weak transcription	Ovary	ovary
11	chr2:172545800-172560200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:172545800-172573000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:172545800-172575400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
15	chr2:172546000-172558600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:172546000-172559200	Weak transcription	Psoas Muscle	Psoas
17	chr2:172546000-172559800	Weak transcription	Fetal Heart	heart
18	chr2:172546000-172560600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:172546000-172563000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:172546000-172567800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:172546000-172568600	Weak transcription	Hela-S3	cervix
22	chr2:172546200-172558400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:172546400-172556600	Weak transcription	Fetal Kidney	kidney
24	chr2:172546400-172561200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:172546400-172574600	Weak transcription	Right Atrium	heart
26	chr2:172546600-172554800	Strong transcription	HSMM	muscle
27	chr2:172546600-172555400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
29	chr2:172546800-172553200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:172546800-172553800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:172546800-172553800	Weak transcription	Brain Substantia Nigra	brain
32	chr2:172546800-172553800	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:172546800-172554800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:172546800-172555000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:172546800-172555200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr2:172546800-172555400	Strong transcription	Fetal Thymus	thymus
37	chr2:172546800-172560400	Weak transcription	Brain Angular Gyrus	brain
38	chr2:172547000-172554800	Strong transcription	NHDF-Ad	bronchial
39	chr2:172547000-172555000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:172547000-172555000	Strong transcription	Placenta	Placenta
41	chr2:172547000-172555400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:172547000-172578600	Weak transcription	Fetal Brain Male	brain
43	chr2:172547200-172554400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:172547200-172554800	Strong transcription	Primary B cells from cord blood	blood
45	chr2:172547200-172554800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:172547200-172555000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:172547200-172555200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:172547200-172555200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:172547200-172560000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:172547200-172561000	Strong transcription	Primary monocytes fromperipheralblood	blood

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