Variant report

Variant	rs6732369
Chromosome Location	chr2:73271874-73271875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:73271756-73271923	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SFXN5	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10166058	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10166220	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10167566	0.80[CEU][hapmap];0.95[JPT][hapmap]
rs10174548	0.90[JPT][hapmap]
rs10176939	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177159	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10178854	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10178944	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10180720	0.87[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10180995	0.80[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs10189744	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10190861	0.80[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs10191665	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10192077	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10197305	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10209859	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1036512	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12233055	0.94[CEU][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13385994	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13388404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13390072	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13393567	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13400920	0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs13400948	0.80[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs13403757	0.91[JPT][hapmap]
rs13403781	0.91[JPT][hapmap]
rs13416407	0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs13424057	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13427947	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1370383	0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1430349	0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs17008571	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17008611	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17008631	0.87[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1864488	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs1992133	0.80[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs2421098	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3813222	0.95[JPT][hapmap]
rs3901273	0.90[JPT][hapmap]
rs4144837	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4514897	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4527230	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55974516	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57536428	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57937746	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58993488	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61161134	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61650913	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62147721	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62147724	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62147732	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546794	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6546796	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546797	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546800	0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs6709938	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6710362	0.83[ASN][1000 genomes]
rs6710739	0.87[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6710755	0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs6711891	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6712925	0.81[AMR][1000 genomes]
rs6713655	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6717553	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719333	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6726940	1.00[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs6727269	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6727919	0.81[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs6729266	0.87[ASW][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap]
rs6736153	0.80[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs6749237	0.95[JPT][hapmap]
rs6750069	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6754779	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6754858	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757131	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759243	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6759733	0.94[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs727470	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs732178	0.94[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs732179	0.94[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs732180	0.86[ASW][hapmap];0.94[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557173	0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs7559340	0.82[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs7566904	0.87[ASW][hapmap];0.87[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7570876	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7578757	0.89[EUR][1000 genomes]
rs7579770	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7580216	0.94[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7597032	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7602651	0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs891432	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs891433	0.81[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs893258	0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs893259	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9309467	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv20443	chr2:73270284-73280427	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6732369	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
2	chr2:73223200-73274600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:73246400-73277400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:73246600-73283800	Weak transcription	Hela-S3	cervix
5	chr2:73247400-73283800	Weak transcription	Dnd41	blood
6	chr2:73248200-73277200	Weak transcription	HMEC	breast
7	chr2:73249200-73276000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:73249400-73284200	Weak transcription	Aorta	Aorta
9	chr2:73249400-73290000	Weak transcription	HUVEC	blood vessel
10	chr2:73249600-73277000	Weak transcription	NH-A	brain
11	chr2:73249600-73290000	Weak transcription	NHLF	lung
12	chr2:73250000-73277200	Weak transcription	HSMMtube	muscle
13	chr2:73250200-73284200	Weak transcription	Ovary	ovary
14	chr2:73250400-73277200	Weak transcription	Placenta	Placenta
15	chr2:73250800-73276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:73253200-73280800	Weak transcription	Fetal Lung	lung
17	chr2:73256800-73279400	Weak transcription	Osteobl	bone
18	chr2:73256800-73280200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:73256800-73290000	Weak transcription	HSMM	muscle
20	chr2:73259200-73291200	Weak transcription	Small Intestine	intestine
21	chr2:73260200-73284200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:73260600-73284400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:73260800-73279200	Weak transcription	Fetal Intestine Large	intestine
24	chr2:73260800-73283800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:73261400-73282000	Weak transcription	Adipose Nuclei	Adipose
26	chr2:73261400-73284200	Weak transcription	Gastric	stomach
27	chr2:73262400-73280400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:73262800-73290600	Weak transcription	NHEK	skin
29	chr2:73263800-73277000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:73263800-73277200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:73264000-73276600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:73264000-73276800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:73264000-73280800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:73264200-73290600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:73264400-73276800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:73264400-73277000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:73264400-73277200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:73264400-73277600	Weak transcription	Fetal Brain Female	brain
39	chr2:73264400-73280000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:73264600-73277200	Weak transcription	Fetal Brain Male	brain
41	chr2:73264600-73284400	Weak transcription	Esophagus	oesophagus
42	chr2:73265600-73276800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:73265600-73283800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:73267400-73276800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:73267800-73289400	Weak transcription	K562	blood
46	chr2:73268000-73280400	Weak transcription	Brain Hippocampus Middle	brain
47	chr2:73268000-73280800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:73268000-73281800	Weak transcription	A549	lung
49	chr2:73268000-73284000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:73268200-73277200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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