Variant report

Variant	rs964267
Chromosome Location	chr5:41810287-41810288
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	chr5:41808159..41810588-chr5:41817487..41819885,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10941559	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11738517	0.94[EUR][1000 genomes]
rs11739106	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11739257	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11740524	0.96[EUR][1000 genomes]
rs11740946	1.00[EUR][1000 genomes]
rs11742249	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11744279	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11744516	1.00[EUR][1000 genomes]
rs11744623	0.97[EUR][1000 genomes]
rs11746511	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11749008	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11750607	0.88[CEU][hapmap];0.82[GIH][hapmap];0.89[EUR][1000 genomes]
rs11750760	0.93[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750790	0.87[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12186512	0.85[ASW][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap]
rs13153468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153837	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13155338	0.85[EUR][1000 genomes]
rs13156367	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13162040	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13163137	1.00[EUR][1000 genomes]
rs13164201	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.84[ASW][hapmap];0.88[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13169285	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13169977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13170096	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13177937	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13179852	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180405	0.88[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180475	0.86[EUR][1000 genomes]
rs13182336	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13186086	0.88[CEU][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs13189403	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1345781	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1389756	0.86[EUR][1000 genomes]
rs1508815	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs16871955	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876653	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876654	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2081102	0.86[EUR][1000 genomes]
rs33967331	1.00[EUR][1000 genomes]
rs34048302	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34071445	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34193394	0.85[EUR][1000 genomes]
rs34329864	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34339137	1.00[EUR][1000 genomes]
rs34369972	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34412181	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34500930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34569700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34625465	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34663371	1.00[EUR][1000 genomes]
rs34841703	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34873414	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34898214	0.85[EUR][1000 genomes]
rs35077044	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs35244816	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35252930	1.00[EUR][1000 genomes]
rs35343042	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35613904	0.97[EUR][1000 genomes]
rs35691805	0.85[EUR][1000 genomes]
rs35748945	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35764180	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35861205	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36009913	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36113900	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3926618	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4957430	1.00[CEU][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs55817686	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56017638	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60209308	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62360521	0.85[EUR][1000 genomes]
rs62360542	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66820325	0.99[EUR][1000 genomes]
rs67114999	1.00[EUR][1000 genomes]
rs67206815	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67715253	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67869805	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865448	0.89[AMR][1000 genomes]
rs6866549	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6879341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6889217	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72746918	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72746919	0.99[EUR][1000 genomes]
rs72746957	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7724934	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7725264	0.82[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs951883	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9687619	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9763018	0.88[AMR][1000 genomes];0.89[EUR][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	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
2	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs964267	LIFR	cis	cerebellum	SCAN
rs964267	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41756200-41813800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:41778200-41838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:41790400-41814000	Weak transcription	Psoas Muscle	Psoas
4	chr5:41793400-41810400	Weak transcription	Spleen	Spleen
5	chr5:41795400-41813000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:41795400-41816200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:41795400-41835800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:41795800-41813000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr5:41796600-41825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:41796600-41830400	Weak transcription	NH-A	brain
11	chr5:41796600-41830600	Weak transcription	NHDF-Ad	bronchial
12	chr5:41796600-41830800	Weak transcription	NHLF	lung
13	chr5:41796800-41812800	Weak transcription	Fetal Brain Female	brain
14	chr5:41797000-41815200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:41797200-41815200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:41800800-41838600	Weak transcription	Fetal Stomach	stomach
17	chr5:41801000-41810800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:41801000-41815800	Weak transcription	Esophagus	oesophagus
19	chr5:41801000-41818000	Weak transcription	Fetal Intestine Large	intestine
20	chr5:41801000-41835800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:41801000-41849200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:41801200-41810400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:41801200-41811200	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:41801200-41811400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr5:41801200-41815800	Weak transcription	Osteobl	bone
26	chr5:41801200-41816000	Weak transcription	HSMMtube	muscle
27	chr5:41801200-41817800	Weak transcription	Small Intestine	intestine
28	chr5:41801200-41849200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:41801200-41849200	Weak transcription	Fetal Brain Male	brain
30	chr5:41801400-41815600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:41801800-41815400	Weak transcription	HSMM	muscle
32	chr5:41804800-41831400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:41805400-41812800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr5:41806800-41810600	Weak transcription	Brain Angular Gyrus	brain
35	chr5:41806800-41816600	Weak transcription	Aorta	Aorta
36	chr5:41807000-41813800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:41807400-41810800	Weak transcription	Lung	lung
38	chr5:41807400-41811000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:41807400-41811000	Weak transcription	Adipose Nuclei	Adipose
40	chr5:41807400-41813200	Weak transcription	K562	blood
41	chr5:41807400-41813200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:41807400-41815400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:41807400-41818000	Weak transcription	Primary B cells from cord blood	blood
44	chr5:41807400-41822200	Weak transcription	Left Ventricle	heart
45	chr5:41807400-41826800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:41807400-41827400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:41807400-41831200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:41807400-41831600	Weak transcription	Thymus	Thymus
49	chr5:41807400-41832000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:41807600-41822600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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