Variant report

Variant	rs7580216
Chromosome Location	chr2:73228999-73229000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73227713..73230641-chr2:73231443..73233674,2	K562	blood:
2	chr2:73227183..73229213-chr2:73231275..73232943,2	K562	blood:
3	chr2:73218918..73222719-chr2:73226745..73229455,3	K562	blood:

Variant related genes	Relation type
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10166058	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10166220	1.00[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10167566	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs10174548	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs10176939	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10177159	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10178854	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10178944	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10180720	0.93[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs10180995	0.81[CEU][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs10189744	1.00[CEU][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10190861	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs10191665	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10192077	0.87[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10197305	0.94[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10209859	0.94[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1036512	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12233055	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621323	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs13385994	0.83[EUR][1000 genomes]
rs13388404	0.94[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13390072	0.83[EUR][1000 genomes]
rs13393567	0.81[EUR][1000 genomes]
rs13400920	0.81[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs13400948	0.80[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap]
rs13403757	0.81[JPT][hapmap]
rs13403781	0.81[JPT][hapmap]
rs13424057	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13427947	0.81[EUR][1000 genomes]
rs1370383	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1430349	0.81[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs17008571	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17008611	0.94[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17008631	0.93[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1864488	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs1992133	0.80[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.90[TSI][hapmap]
rs2421098	0.91[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3813222	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs3901273	0.81[JPT][hapmap]
rs4144837	0.93[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4514897	0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4527230	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55974516	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57536428	0.83[EUR][1000 genomes]
rs57937746	0.83[EUR][1000 genomes]
rs58993488	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61161134	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61650913	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62147721	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62147724	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62147732	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546794	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546796	0.94[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546797	0.94[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6546800	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs6709938	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6710362	0.83[ASN][1000 genomes]
rs6710739	0.93[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs6711891	0.94[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs6713655	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6717553	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719333	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6726940	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727269	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6727919	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs6729266	0.80[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs6732369	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]
rs6736153	0.80[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs6749237	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs6750069	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6754779	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6754858	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6757131	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6759243	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6759733	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs727470	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs732178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7557173	0.80[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs7559340	0.81[CEU][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7566904	0.93[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7570876	0.94[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7578757	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7579770	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7597032	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602651	0.81[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs891432	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs891433	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs893258	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs893259	0.94[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309467	0.99[EUR][1000 genomes];0.93[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7580216	SFXN5	cis	cerebellum	SCAN
rs7580216	RAB11FIP5	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73190600-73234400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:73194200-73248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:73208000-73247600	Weak transcription	Primary B cells from cord blood	blood
5	chr2:73211000-73258400	Weak transcription	Colonic Mucosa	Colon
6	chr2:73211600-73235800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:73212200-73247400	Weak transcription	HSMMtube	muscle
8	chr2:73212400-73236000	Weak transcription	Esophagus	oesophagus
9	chr2:73212800-73238800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:73213800-73236200	Weak transcription	Pancreas	Pancrea
11	chr2:73214000-73232000	Weak transcription	Aorta	Aorta
12	chr2:73214000-73238400	Weak transcription	Fetal Lung	lung
13	chr2:73214200-73247800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
15	chr2:73215400-73236000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:73215800-73235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:73215800-73247400	Weak transcription	Thymus	Thymus
18	chr2:73215800-73263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:73216000-73236000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:73216200-73248800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:73216800-73234400	Weak transcription	Primary T cells from cord blood	blood
22	chr2:73217400-73231800	Weak transcription	Fetal Heart	heart
23	chr2:73217400-73236200	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:73217400-73249000	Weak transcription	Ovary	ovary
25	chr2:73217800-73237400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:73220600-73249000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:73220600-73263200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:73221200-73231400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:73221200-73263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:73222200-73229000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:73223000-73229200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:73223200-73229600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:73223200-73274600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:73223400-73232200	Weak transcription	Fetal Brain Female	brain
35	chr2:73223400-73232800	Weak transcription	Brain Germinal Matrix	brain
36	chr2:73223600-73232400	Weak transcription	Brain Angular Gyrus	brain
37	chr2:73223600-73235400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:73224600-73261200	Weak transcription	Brain Substantia Nigra	brain
39	chr2:73225400-73229000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:73226200-73236200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:73226200-73248800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:73226400-73236400	Weak transcription	Brain Anterior Caudate	brain
43	chr2:73226600-73236000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:73226800-73229000	Enhancers	Fetal Intestine Large	intestine
45	chr2:73227400-73229000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:73227600-73230000	Genic enhancers	HepG2	liver
47	chr2:73227600-73249000	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:73227800-73233800	Weak transcription	HUVEC	blood vessel
49	chr2:73227800-73234000	Weak transcription	K562	blood
50	chr2:73227800-73235000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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