Variant report

Variant	rs34625465
Chromosome Location	chr5:41792289-41792290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11738517	0.94[EUR][1000 genomes]
rs11739106	0.93[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	0.84[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	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11747881	0.92[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];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11749008	0.89[AFR][1000 genomes];0.96[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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750790	0.87[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12186512	0.88[LWK][hapmap];0.91[MKK][hapmap]
rs13153468	0.92[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13153837	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13155013	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13155338	0.85[EUR][1000 genomes]
rs13156367	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13162040	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13163137	1.00[EUR][1000 genomes]
rs13164201	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13165731	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13167578	0.88[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13169285	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13169977	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13170096	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13177937	0.92[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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13179852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13180405	0.88[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13180475	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13182336	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[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	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1345781	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1389756	0.86[EUR][1000 genomes]
rs1508815	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs16871955	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876653	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1876654	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2081102	0.86[EUR][1000 genomes]
rs33967331	1.00[EUR][1000 genomes]
rs34048302	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34071445	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34193394	0.85[EUR][1000 genomes]
rs34329864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34339137	1.00[EUR][1000 genomes]
rs34369972	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34412181	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34500930	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34569700	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34663371	1.00[EUR][1000 genomes]
rs34841703	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34873414	0.92[AFR][1000 genomes];1.00[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	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35252930	1.00[EUR][1000 genomes]
rs35343042	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35613904	0.97[EUR][1000 genomes]
rs35691805	0.85[EUR][1000 genomes]
rs35748945	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35764180	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35861205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005620	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36009913	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36113900	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3926618	0.93[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[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56017638	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60209308	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62360521	0.85[EUR][1000 genomes]
rs62360542	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66820325	0.99[EUR][1000 genomes]
rs67114999	1.00[EUR][1000 genomes]
rs67206815	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67715253	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67869805	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6865448	0.82[AMR][1000 genomes]
rs6866549	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6879341	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888816	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6889217	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72746918	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72746919	0.99[EUR][1000 genomes]
rs72746957	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709500	0.92[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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7724934	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7725264	0.82[CEU][hapmap];1.00[MEX][hapmap];0.87[EUR][1000 genomes]
rs951883	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs964267	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9687619	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9763018	0.81[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
rs34625465	OXCT1	Cis_1M	lymphoblastoid	RTeQTL
rs34625465	LIFR	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41731400-41800400	Weak transcription	Small Intestine	intestine
2	chr5:41735800-41800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:41739400-41799600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:41739600-41794800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:41749200-41797800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:41756200-41813800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:41759800-41800400	Weak transcription	Esophagus	oesophagus
8	chr5:41761200-41798400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:41761600-41804600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:41761800-41795000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:41762000-41799600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:41762200-41794200	Weak transcription	Adipose Nuclei	Adipose
13	chr5:41762400-41794400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:41763800-41793200	Weak transcription	NHEK	skin
15	chr5:41764000-41794600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:41765000-41793000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:41765000-41793200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:41770000-41794600	Weak transcription	Thymus	Thymus
19	chr5:41776000-41792600	Weak transcription	GM12878-XiMat	blood
20	chr5:41776000-41798200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:41776400-41793400	Weak transcription	Brain Angular Gyrus	brain
22	chr5:41778200-41838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:41779000-41795200	Weak transcription	Lung	lung
24	chr5:41780000-41800200	Weak transcription	Fetal Intestine Large	intestine
25	chr5:41784000-41795000	Weak transcription	Right Ventricle	heart
26	chr5:41784200-41793200	Weak transcription	HMEC	breast
27	chr5:41784600-41792400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:41784600-41794400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:41784800-41796200	Weak transcription	K562	blood
30	chr5:41785600-41794400	Weak transcription	Fetal Kidney	kidney
31	chr5:41785800-41800000	Weak transcription	Fetal Brain Male	brain
32	chr5:41786400-41795200	Weak transcription	Left Ventricle	heart
33	chr5:41786600-41794000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:41786600-41794400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:41786600-41795000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:41787000-41792400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr5:41787000-41793000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:41787400-41792400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:41787800-41794400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:41788000-41792400	Weak transcription	Dnd41	blood
41	chr5:41788000-41794200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:41788000-41794200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:41788400-41794400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:41788600-41800000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:41789400-41795000	Weak transcription	Ovary	ovary
46	chr5:41789600-41794400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:41789600-41808200	Weak transcription	Fetal Intestine Small	intestine
48	chr5:41789800-41793000	Weak transcription	A549	lung
49	chr5:41789800-41794200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:41790200-41793400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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