Variant report

Variant	rs16871955
Chromosome Location	chr5:41805575-41805576
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:41800412..41802108-chr5:41804338..41806485,2	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[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11738517	0.94[EUR][1000 genomes]
rs11739106	0.84[AFR][1000 genomes];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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11749008	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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750790	0.87[CEU][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12186512	0.85[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs13153468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153837	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.81[AFR][1000 genomes];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	0.93[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	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	0.82[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	0.82[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	0.82[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];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13179852	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180405	0.88[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180475	0.86[EUR][1000 genomes]
rs13182336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13186086	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13189403	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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];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	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34193394	0.85[EUR][1000 genomes]
rs34329864	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34339137	1.00[EUR][1000 genomes]
rs34369972	1.00[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34569700	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34625465	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34663371	1.00[EUR][1000 genomes]
rs34841703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34873414	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	0.87[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	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35861205	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005620	0.82[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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3926618	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	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56017638	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60209308	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	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67715253	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67869805	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865448	0.89[AMR][1000 genomes]
rs6866549	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6879341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888816	0.83[AFR][1000 genomes];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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709500	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7724934	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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964267	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9687619	1.00[CEU][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
rs16871955	LIFR	cis	cerebellum	SCAN
rs16871955	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 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	chr5:41789600-41808200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:41790400-41814000	Weak transcription	Psoas Muscle	Psoas
5	chr5:41791600-41807600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr5:41793400-41810400	Weak transcription	Spleen	Spleen
7	chr5:41795200-41805800	Weak transcription	Brain Angular Gyrus	brain
8	chr5:41795400-41809400	Weak transcription	Fetal Kidney	kidney
9	chr5:41795400-41809800	Weak transcription	Brain Anterior Caudate	brain
10	chr5:41795400-41813000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:41795400-41816200	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:41795400-41835800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:41795600-41805600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:41795600-41806000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:41795600-41806600	Weak transcription	Lung	lung
16	chr5:41795600-41808000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:41795600-41808600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:41795600-41809000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:41795800-41809000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:41795800-41813000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:41796600-41808800	Weak transcription	Fetal Heart	heart
22	chr5:41796600-41825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:41796600-41830400	Weak transcription	NH-A	brain
24	chr5:41796600-41830600	Weak transcription	NHDF-Ad	bronchial
25	chr5:41796600-41830800	Weak transcription	NHLF	lung
26	chr5:41796800-41812800	Weak transcription	Fetal Brain Female	brain
27	chr5:41797000-41815200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:41797200-41805600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:41797200-41815200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:41797600-41809000	Strong transcription	Dnd41	blood
31	chr5:41798000-41807800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:41798600-41808800	Strong transcription	Hela-S3	cervix
33	chr5:41800800-41808400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:41800800-41810200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:41800800-41838600	Weak transcription	Fetal Stomach	stomach
36	chr5:41801000-41808200	Weak transcription	Gastric	stomach
37	chr5:41801000-41809600	Weak transcription	Right Ventricle	heart
38	chr5:41801000-41810200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:41801000-41810800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:41801000-41815800	Weak transcription	Esophagus	oesophagus
41	chr5:41801000-41818000	Weak transcription	Fetal Intestine Large	intestine
42	chr5:41801000-41835800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:41801000-41849200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:41801200-41805600	Weak transcription	Aorta	Aorta
45	chr5:41801200-41805600	Weak transcription	Left Ventricle	heart
46	chr5:41801200-41805800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:41801200-41806000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr5:41801200-41806200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:41801200-41806400	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:41801200-41808200	Weak transcription	Ovary	ovary

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