Variant report

Variant	rs6879341
Chromosome Location	chr5:41839180-41839181
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:41837142..41840023-chr5:41841015..41842990,3	K562	blood:
2	chr5:41835392..41837022-chr5:41838545..41840862,2	K562	blood:

Variant related genes	Relation type
ENSG00000083720	Chromatin interaction

Extended variants
information (count: 111 )
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	0.88[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	0.88[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];1.00[MEX][hapmap];0.83[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];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750790	0.87[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12186512	0.85[ASW][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.91[YRI][hapmap]
rs13153468	1.00[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]
rs13153837	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	0.93[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];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13168035	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13169285	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13169977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13170096	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13176368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13177937	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];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	0.83[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	0.85[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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1508818	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs16871955	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16871972	0.99[EUR][1000 genomes]
rs16900142	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[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[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	0.83[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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34569700	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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005620	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	0.84[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]
rs6881206	0.85[EUR][1000 genomes]
rs6881873	0.99[EUR][1000 genomes]
rs6883144	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6888816	1.00[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	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709500	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]
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	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:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6879341	LIFR	cis	cerebellum	SCAN
rs6879341	OXCT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41801000-41849200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:41801200-41849200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:41801200-41849200	Weak transcription	Fetal Brain Male	brain
4	chr5:41814000-41842200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:41818400-41852000	Weak transcription	Small Intestine	intestine
6	chr5:41819200-41852800	Weak transcription	Pancreas	Pancrea
7	chr5:41822600-41849200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
9	chr5:41825800-41849200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:41827800-41849800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:41828600-41849200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:41828800-41849000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:41829400-41851000	Weak transcription	Fetal Intestine Small	intestine
14	chr5:41830000-41843400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:41830800-41849200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:41830800-41849800	Weak transcription	Gastric	stomach
17	chr5:41831200-41849200	Weak transcription	Brain Germinal Matrix	brain
18	chr5:41831200-41854400	Weak transcription	Colonic Mucosa	Colon
19	chr5:41831400-41849200	Weak transcription	Placenta	Placenta
20	chr5:41832200-41849200	Weak transcription	Fetal Kidney	kidney
21	chr5:41832400-41842400	Weak transcription	Fetal Lung	lung
22	chr5:41832400-41842600	Weak transcription	K562	blood
23	chr5:41832800-41849200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:41832800-41850000	Weak transcription	Esophagus	oesophagus
25	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:41833400-41849200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr5:41834000-41849200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:41834200-41839600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:41834600-41849200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:41835800-41843200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:41835800-41845600	Strong transcription	Dnd41	blood
32	chr5:41836000-41857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:41836200-41839800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:41836200-41839800	Weak transcription	HMEC	breast
35	chr5:41836200-41849200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:41836400-41841200	Weak transcription	Aorta	Aorta
37	chr5:41836400-41841200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:41836400-41841400	Weak transcription	NHLF	lung
39	chr5:41836400-41842600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:41836400-41843600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:41836400-41849200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:41836400-41849200	Weak transcription	Brain Anterior Caudate	brain
43	chr5:41836400-41849200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:41836400-41849200	Weak transcription	Brain Substantia Nigra	brain
45	chr5:41836400-41849200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:41836400-41849200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:41836400-41849400	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:41836600-41840000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:41836600-41843400	Strong transcription	Hela-S3	cervix
50	chr5:41836600-41849000	Weak transcription	NHDF-Ad	bronchial

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