Variant report

Variant	rs6451581
Chromosome Location	chr5:41754094-41754095
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	chr5:41747189..41749096-chr5:41753764..41755321,2	K562	blood:
2	chr5:41748253..41750821-chr5:41752950..41755627,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10045473	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10059424	1.00[JPT][hapmap]
rs10060170	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10062703	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10064298	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10064380	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10069638	1.00[JPT][hapmap]
rs1006996	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10070201	1.00[JPT][hapmap]
rs10075064	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10077481	1.00[JPT][hapmap]
rs10472357	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10941557	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1118104	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11738517	0.93[ASN][1000 genomes]
rs11739257	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11740524	0.86[ASN][1000 genomes]
rs11740946	1.00[ASN][1000 genomes]
rs11744279	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11744623	0.86[ASN][1000 genomes]
rs11745373	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11747921	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1175227	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13163137	1.00[ASN][1000 genomes]
rs13360001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1355089	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1494392	1.00[ASN][1000 genomes]
rs1508816	0.90[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1533014	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16871940	1.00[ASN][1000 genomes]
rs16871972	0.86[ASN][1000 genomes]
rs17739462	0.86[ASN][1000 genomes]
rs17847285	0.86[ASN][1000 genomes]
rs1876654	1.00[JPT][hapmap]
rs2231910	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2329815	0.86[ASN][1000 genomes]
rs277406	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs277407	0.87[EUR][1000 genomes]
rs277414	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs277416	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2910628	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs316723	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316724	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs316730	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316744	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316745	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs316751	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs316760	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33967331	1.00[ASN][1000 genomes]
rs34339137	0.86[ASN][1000 genomes]
rs34602857	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34663371	0.86[ASN][1000 genomes]
rs35077044	1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs35154057	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35613904	0.86[ASN][1000 genomes]
rs35795768	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4050986	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4245982	1.00[ASN][1000 genomes]
rs4289604	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4324728	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4957171	1.00[JPT][hapmap]
rs4957173	1.00[JPT][hapmap]
rs4957174	1.00[JPT][hapmap]
rs4957175	1.00[JPT][hapmap]
rs4957176	1.00[JPT][hapmap]
rs4957177	1.00[JPT][hapmap]
rs4957419	1.00[ASN][1000 genomes]
rs4957420	0.83[AFR][1000 genomes]
rs4957422	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4957423	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4957424	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4957428	0.86[ASN][1000 genomes]
rs4957429	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4957430	0.81[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs4957431	1.00[JPT][hapmap]
rs4957432	1.00[JPT][hapmap]
rs4957434	1.00[JPT][hapmap]
rs4957435	1.00[JPT][hapmap]
rs4957436	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4957437	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4957438	1.00[JPT][hapmap]
rs608902	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs622413	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs624097	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451582	0.90[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66820325	0.86[ASN][1000 genomes]
rs67114999	0.86[ASN][1000 genomes]
rs676067	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6881873	0.86[ASN][1000 genomes]
rs6889217	1.00[JPT][hapmap]
rs7712911	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7728482	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7729014	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7733096	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9292825	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[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	nsv830271	chr5:41716527-41895710	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6451581	C5orf39	cis	cerebellum	SCAN
rs6451581	LIFR	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41727800-41758200	Weak transcription	Esophagus	oesophagus
2	chr5:41728600-41763800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:41729200-41755000	Weak transcription	NHDF-Ad	bronchial
4	chr5:41730200-41764000	Weak transcription	Spleen	Spleen
5	chr5:41730600-41760800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:41731400-41800400	Weak transcription	Small Intestine	intestine
7	chr5:41734600-41757800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:41735600-41763200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:41735600-41763400	Weak transcription	Fetal Brain Male	brain
10	chr5:41735800-41800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:41736200-41763400	Weak transcription	Psoas Muscle	Psoas
12	chr5:41736800-41763000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:41737000-41754800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:41737800-41763400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:41738800-41755800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:41738800-41759600	Weak transcription	Ovary	ovary
17	chr5:41738800-41760800	Weak transcription	NHEK	skin
18	chr5:41739200-41763200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:41739400-41754800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:41739400-41759000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:41739400-41770800	Weak transcription	Pancreas	Pancrea
22	chr5:41739400-41788800	Weak transcription	Gastric	stomach
23	chr5:41739400-41790200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:41739400-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:41739600-41757400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:41739600-41758200	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:41739600-41761200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:41739600-41764000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:41739600-41764600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:41739600-41765200	Weak transcription	Lung	lung
31	chr5:41739600-41768000	Weak transcription	Right Ventricle	heart
32	chr5:41739600-41786400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:41739600-41794800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:41739800-41770400	Weak transcription	Fetal Stomach	stomach
35	chr5:41740600-41754800	Weak transcription	HMEC	breast
36	chr5:41746000-41754200	Strong transcription	Primary T cells from cord blood	blood
37	chr5:41747000-41762800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:41747000-41784000	Weak transcription	K562	blood
39	chr5:41747400-41777600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:41747600-41760800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:41747800-41762800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:41747800-41766400	Weak transcription	Brain Angular Gyrus	brain
43	chr5:41748000-41755000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:41748000-41760800	Weak transcription	Fetal Kidney	kidney
45	chr5:41748200-41762000	Weak transcription	Fetal Lung	lung
46	chr5:41748200-41762200	Weak transcription	NHLF	lung
47	chr5:41748200-41762600	Weak transcription	NH-A	brain
48	chr5:41748200-41776000	Weak transcription	HUVEC	blood vessel
49	chr5:41748400-41759000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr5:41748400-41761200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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