Variant report

Variant	rs4497004
Chromosome Location	chr8:66609549-66609550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:66545047..66547819-chr8:66607302..66610093,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE7A-2	chr8:66609517-66609653	ucscGeneNc_uc003xvk_1

Variant related genes	Relation type
ENSG00000104442	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1022253	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1022254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11995337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];1.00[ASN][1000 genomes]
rs16932294	0.82[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17303905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17394924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2175810	0.81[LWK][hapmap]
rs2357478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35524385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41343545	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56698878	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57220512	0.97[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs57962817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58398396	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58594670	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60824178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66773449	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66817670	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66820398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66824691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66901832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66908793	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67125822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67202221	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67362541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67433957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67445866	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67514002	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67578481	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67669255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67686346	0.87[EUR][1000 genomes]
rs67692803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68075342	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68087267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68167505	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002171	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7002494	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7002953	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72666512	1.00[ASN][1000 genomes]
rs72666522	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72666525	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239047	1.00[ASN][1000 genomes]
rs73239052	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73239095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73240732	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463538	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825615	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7842162	0.81[LWK][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4497004	MTFR1	Cis_1M	lymphoblastoid	RTeQTL
rs4497004	MTFR1	cis	cerebellum	SCAN
rs4497004	ARMC1	cis	parietal	SCAN
rs4497004	MTFR1	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66567200-66616800	Weak transcription	Gastric	stomach
2	chr8:66571800-66616800	Weak transcription	Esophagus	oesophagus
3	chr8:66571800-66619600	Weak transcription	Brain Hippocampus Middle	brain
4	chr8:66572000-66611400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:66572000-66612800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:66572000-66616600	Weak transcription	HMEC	breast
7	chr8:66572000-66617000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:66572000-66617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr8:66572000-66617800	Weak transcription	NHDF-Ad	bronchial
10	chr8:66572000-66619600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr8:66572000-66619600	Weak transcription	NHEK	skin
12	chr8:66572000-66619800	Weak transcription	Lung	lung
13	chr8:66572000-66628400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr8:66572200-66619800	Weak transcription	A549	lung
15	chr8:66573800-66615200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:66573800-66630400	Weak transcription	Spleen	Spleen
17	chr8:66574400-66616800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:66579000-66611200	Weak transcription	Pancreas	Pancrea
19	chr8:66580000-66619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:66580400-66618600	Weak transcription	Osteobl	bone
21	chr8:66580400-66619800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr8:66580600-66619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr8:66581000-66609600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr8:66581000-66619600	Weak transcription	Fetal Lung	lung
25	chr8:66581200-66619400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr8:66582000-66616800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr8:66582200-66616800	Weak transcription	Right Ventricle	heart
28	chr8:66582800-66617800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr8:66583000-66616800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:66583600-66619800	Weak transcription	Brain Angular Gyrus	brain
31	chr8:66583800-66610800	Weak transcription	Fetal Stomach	stomach
32	chr8:66583800-66619800	Weak transcription	Aorta	Aorta
33	chr8:66584200-66620000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr8:66584800-66619800	Weak transcription	Brain Germinal Matrix	brain
35	chr8:66584800-66628600	Weak transcription	NHLF	lung
36	chr8:66585000-66617400	Weak transcription	HepG2	liver
37	chr8:66585600-66619400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr8:66587800-66628000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr8:66588200-66619600	Weak transcription	Brain Anterior Caudate	brain
40	chr8:66590200-66619800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:66591400-66617800	Weak transcription	Colon Smooth Muscle	Colon
42	chr8:66591600-66619800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr8:66592600-66615000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr8:66593400-66628400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr8:66593800-66630000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr8:66595400-66616600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr8:66595400-66619600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr8:66596200-66619400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:66596400-66612800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr8:66596600-66617000	Weak transcription	Hela-S3	cervix

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