Variant report

Variant	rs6433311
Chromosome Location	chr2:172549248-172549249
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	chr2:172544067..172546213-chr2:172547195..172550116,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077380	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	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10167419	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10174525	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10184866	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10194102	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10200608	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10201419	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10204502	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10204622	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206062	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10207085	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10497374	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10803863	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1113389	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11678984	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11757	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11886820	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11897196	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11904009	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12053003	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12185567	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692970	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12692973	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12692974	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12692978	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13017585	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13018768	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13022113	0.89[EUR][1000 genomes]
rs13419987	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13429113	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13429409	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1474074	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1554166	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1973706	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292815	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2357061	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2674484	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2678155	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs312916	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312918	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs312919	0.89[AMR][1000 genomes]
rs312921	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs312924	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs312925	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34358700	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34542126	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35379278	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35391289	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35549875	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35645520	0.82[AMR][1000 genomes]
rs35854280	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36057702	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770445	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3770451	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3770452	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3795999	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667693	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667694	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4668407	0.81[EUR][1000 genomes]
rs4668412	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4668414	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6433314	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66835971	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6705200	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6709156	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6710698	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67204065	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6721680	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6722757	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6724337	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6725388	0.81[AMR][1000 genomes]
rs6738445	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6745143	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6754817	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6757773	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758704	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6759575	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71013062	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7355523	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7355594	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7562356	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7572215	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7586207	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7597387	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7604918	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608403	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs908670	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs908671	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs973889	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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
rs6433311	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6433311	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6433311	AC068039.4	cis	Muscle Skeletal	GTEx
rs6433311	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6433311	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6433311	AC068039.4	cis	Thyroid	GTEx
rs6433311	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6433311	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6433311	AC068039.4	cis	Whole Blood	GTEx
rs6433311	AC068039.4	cis	Nerve Tibial	GTEx
rs6433311	AC068039.4	cis	Stomach	GTEx
rs6433311	AC068039.4	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:172545000-172550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:172545000-172550600	Weak transcription	Lung	lung
4	chr2:172545000-172553600	Weak transcription	Esophagus	oesophagus
5	chr2:172545000-172553600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
7	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
8	chr2:172545000-172580800	Weak transcription	Gastric	stomach
9	chr2:172545200-172550600	Weak transcription	Left Ventricle	heart
10	chr2:172545200-172551600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:172545600-172550000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:172545600-172550600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:172545600-172550600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:172545600-172551200	Weak transcription	Colonic Mucosa	Colon
17	chr2:172545800-172550600	Weak transcription	Fetal Stomach	stomach
18	chr2:172545800-172550600	Weak transcription	Thymus	Thymus
19	chr2:172545800-172551000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:172545800-172551200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:172545800-172551400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:172545800-172553600	Weak transcription	Aorta	Aorta
23	chr2:172545800-172553800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:172545800-172556600	Weak transcription	Ovary	ovary
25	chr2:172545800-172560200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:172545800-172573000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:172545800-172575400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
29	chr2:172546000-172551000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:172546000-172551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:172546000-172551200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:172546000-172551200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:172546000-172558600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:172546000-172559200	Weak transcription	Psoas Muscle	Psoas
35	chr2:172546000-172559800	Weak transcription	Fetal Heart	heart
36	chr2:172546000-172560600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:172546000-172563000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:172546000-172567800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:172546000-172568600	Weak transcription	Hela-S3	cervix
40	chr2:172546200-172549600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:172546200-172550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:172546200-172550000	Weak transcription	Adipose Nuclei	Adipose
43	chr2:172546200-172551000	Weak transcription	HSMMtube	muscle
44	chr2:172546200-172551200	Weak transcription	Primary T cells from cord blood	blood
45	chr2:172546200-172558400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:172546400-172549800	Weak transcription	Brain Germinal Matrix	brain
47	chr2:172546400-172556600	Weak transcription	Fetal Kidney	kidney
48	chr2:172546400-172561200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:172546400-172574600	Weak transcription	Right Atrium	heart
50	chr2:172546600-172551000	Weak transcription	NHLF	lung

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