Variant report

Variant	rs11744623
Chromosome Location	chr5:41854877-41854878
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	chr5:41850949..41853870-chr5:41854462..41856684,2	MCF-7	breast:

Extended variants
information (count: 185 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:181)

rs_ID	r²[population]
rs10045473	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10051322	0.93[ASN][1000 genomes]
rs10059424	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10060170	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10062703	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10064298	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10064380	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10069638	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1006996	1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs10070201	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10075064	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10077481	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10472357	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10941557	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10941559	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1118104	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11738517	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11739106	0.99[EUR][1000 genomes]
rs11739257	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740524	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740946	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11742249	0.90[EUR][1000 genomes]
rs11744279	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744516	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11745373	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11746511	0.99[EUR][1000 genomes]
rs11747881	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs11747921	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749008	0.95[EUR][1000 genomes]
rs11750607	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11750760	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs11750790	0.87[CEU][hapmap];0.97[EUR][1000 genomes]
rs1175227	0.93[ASN][1000 genomes]
rs13153468	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs13153837	0.99[EUR][1000 genomes]
rs13155013	0.83[EUR][1000 genomes]
rs13155338	0.83[EUR][1000 genomes]
rs13156367	0.90[EUR][1000 genomes]
rs13162040	0.97[EUR][1000 genomes]
rs13163137	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13164201	0.99[EUR][1000 genomes]
rs13165731	0.98[EUR][1000 genomes]
rs13167578	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs13168035	0.97[EUR][1000 genomes]
rs13169285	0.90[EUR][1000 genomes]
rs13169977	0.97[EUR][1000 genomes]
rs13170096	0.93[EUR][1000 genomes]
rs13176368	0.97[EUR][1000 genomes]
rs13177937	0.89[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs13179852	0.97[EUR][1000 genomes]
rs13180405	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs13180475	0.83[EUR][1000 genomes]
rs13182336	0.97[EUR][1000 genomes]
rs13185973	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13186086	0.83[EUR][1000 genomes]
rs13189403	0.92[EUR][1000 genomes]
rs13357951	0.93[ASN][1000 genomes]
rs13360001	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1345781	0.92[EUR][1000 genomes]
rs1355089	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1389756	0.83[EUR][1000 genomes]
rs1494392	0.86[ASN][1000 genomes]
rs1508815	0.97[EUR][1000 genomes]
rs1508816	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs1533014	1.00[ASN][1000 genomes]
rs16871940	0.86[ASN][1000 genomes]
rs16871955	0.97[EUR][1000 genomes]
rs16871972	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16900142	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17739462	1.00[ASN][1000 genomes]
rs17847285	1.00[ASN][1000 genomes]
rs1876653	1.00[EUR][1000 genomes]
rs1876654	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2081102	0.83[EUR][1000 genomes]
rs2113053	0.93[ASN][1000 genomes]
rs2231910	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2231917	0.93[ASN][1000 genomes]
rs2329815	1.00[ASN][1000 genomes]
rs277406	0.93[ASN][1000 genomes]
rs277407	0.93[ASN][1000 genomes]
rs277414	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs277416	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs316760	0.86[ASN][1000 genomes]
rs33967331	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34048302	0.90[EUR][1000 genomes]
rs34071445	0.97[EUR][1000 genomes]
rs34193394	0.83[EUR][1000 genomes]
rs34329864	0.97[EUR][1000 genomes]
rs34339137	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34369972	0.97[EUR][1000 genomes]
rs34412181	0.95[EUR][1000 genomes]
rs34500930	0.97[EUR][1000 genomes]
rs34569700	0.97[EUR][1000 genomes]
rs34625465	0.97[EUR][1000 genomes]
rs34663371	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34841703	0.97[EUR][1000 genomes]
rs34873414	0.97[EUR][1000 genomes]
rs34898214	0.83[EUR][1000 genomes]
rs35077044	1.00[ASW][hapmap];1.00[CEU][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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154057	1.00[ASN][1000 genomes]
rs35244816	0.89[EUR][1000 genomes]
rs35252930	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35343042	0.96[EUR][1000 genomes]
rs35613904	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35691805	0.83[EUR][1000 genomes]
rs35748945	0.92[EUR][1000 genomes]
rs35764180	0.96[EUR][1000 genomes]
rs35861205	0.97[EUR][1000 genomes]
rs36005620	0.97[EUR][1000 genomes]
rs36009913	0.90[EUR][1000 genomes]
rs36113900	0.97[EUR][1000 genomes]
rs3926618	0.97[EUR][1000 genomes]
rs4050986	1.00[ASN][1000 genomes]
rs4245982	0.86[ASN][1000 genomes]
rs4289604	0.93[ASN][1000 genomes]
rs4324728	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4957171	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957173	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957174	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957175	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957176	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957177	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957178	0.93[ASN][1000 genomes]
rs4957180	0.93[ASN][1000 genomes]
rs4957419	0.86[ASN][1000 genomes]
rs4957422	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957423	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957424	1.00[ASN][1000 genomes]
rs4957428	1.00[ASN][1000 genomes]
rs4957429	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4957430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957431	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957432	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957433	0.93[ASN][1000 genomes]
rs4957434	1.00[JPT][hapmap]
rs4957435	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957436	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957437	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957438	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4957439	0.93[ASN][1000 genomes]
rs55817686	0.96[EUR][1000 genomes]
rs56017638	0.97[EUR][1000 genomes]
rs60209308	0.97[EUR][1000 genomes]
rs62360521	0.83[EUR][1000 genomes]
rs62360542	0.91[EUR][1000 genomes]
rs626907	1.00[JPT][hapmap]
rs6451581	0.86[ASN][1000 genomes]
rs6451582	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs66820325	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67114999	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67206815	0.96[EUR][1000 genomes]
rs676067	0.93[ASN][1000 genomes]
rs67715253	0.96[EUR][1000 genomes]
rs67869805	0.99[EUR][1000 genomes]
rs6865448	0.82[EUR][1000 genomes]
rs6866549	0.97[EUR][1000 genomes]
rs6879341	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6881206	0.87[EUR][1000 genomes]
rs6881873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883144	0.97[EUR][1000 genomes]
rs6888816	0.97[EUR][1000 genomes]
rs6889217	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72746918	0.96[EUR][1000 genomes]
rs72746919	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72746957	0.97[EUR][1000 genomes]
rs72746983	0.93[ASN][1000 genomes]
rs72746996	0.93[ASN][1000 genomes]
rs7709500	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7712911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721136	0.82[EUR][1000 genomes]
rs7724934	0.96[EUR][1000 genomes]
rs7725264	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs7728482	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7729014	1.00[ASN][1000 genomes]
rs7733096	1.00[ASN][1000 genomes]
rs9292825	0.93[ASN][1000 genomes]
rs951883	0.97[EUR][1000 genomes]
rs964267	0.97[EUR][1000 genomes]
rs9687619	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9763018	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv4811	chr5:41844522-41887353	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11744623	LIFR	cis	cerebellum	SCAN
rs11744623	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
2	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:41836000-41857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:41836600-41863800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr5:41837200-41858600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:41841800-41869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:41843800-41855600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:41849000-41855200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:41849000-41856000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:41849000-41856200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:41849000-41856400	Strong transcription	Adipose Nuclei	Adipose
12	chr5:41849000-41856600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:41849000-41856600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:41849000-41857000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:41849000-41857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:41849000-41857200	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:41849000-41857200	Strong transcription	K562	blood
18	chr5:41849000-41857800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:41849000-41862200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:41849000-41862600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:41849000-41862800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr5:41849000-41862800	Strong transcription	Fetal Thymus	thymus
23	chr5:41849200-41855400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:41849200-41855600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:41849200-41855800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:41849200-41855800	Strong transcription	HUVEC	blood vessel
27	chr5:41849200-41856200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:41849200-41856400	Strong transcription	Primary B cells from cord blood	blood
29	chr5:41849200-41856400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:41849200-41856600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:41849200-41856600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:41849200-41856600	Strong transcription	NHEK	skin
33	chr5:41849200-41856800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr5:41849200-41857000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:41849200-41859200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:41849200-41862000	Strong transcription	Dnd41	blood
37	chr5:41849200-41862400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:41849200-41862800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:41849200-41863600	Strong transcription	Hela-S3	cervix
40	chr5:41849600-41856200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:41849800-41856400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:41849800-41864000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:41849800-41869000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:41850200-41856800	Strong transcription	GM12878-XiMat	blood
45	chr5:41850400-41857000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:41850400-41864200	Weak transcription	Brain Angular Gyrus	brain
47	chr5:41850400-41868800	Weak transcription	Fetal Brain Male	brain
48	chr5:41850400-41869000	Weak transcription	Esophagus	oesophagus
49	chr5:41850400-41869000	Weak transcription	Fetal Heart	heart
50	chr5:41850400-41869000	Weak transcription	Rectal Mucosa Donor 31	rectum

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