Variant report

Variant	rs1011266
Chromosome Location	chr1:169647046-169647047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169642958..169645181-chr1:169646382..169648638,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10489183	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10919204	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10919207	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10919208	0.85[ASN][1000 genomes]
rs10919214	0.85[ASN][1000 genomes]
rs10919216	0.85[ASN][1000 genomes]
rs10919219	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11487513	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12067152	0.82[ASN][1000 genomes]
rs12076747	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12081319	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12087424	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12116738	1.00[AFR][1000 genomes]
rs12116948	0.85[ASN][1000 genomes]
rs12116974	0.86[ASN][1000 genomes]
rs12123695	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12126695	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12131631	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12140128	0.86[ASN][1000 genomes]
rs1569474	0.86[ASN][1000 genomes]
rs1569476	0.90[ASN][1000 genomes]
rs1800805	0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs1800808	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236868	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs28409897	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3917408	1.00[LWK][hapmap]
rs3917655	0.85[ASN][1000 genomes]
rs3917657	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3917675	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs3917681	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3917682	0.93[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3917702	0.82[ASN][1000 genomes]
rs3917709	1.00[ASW][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs3917729	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58647626	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60035985	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6124	1.00[LWK][hapmap]
rs6131	0.81[JPT][hapmap]
rs66920835	0.90[ASN][1000 genomes]
rs9332605	1.00[LWK][hapmap]

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	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1011266	C1orf156	cis	lymphoblastoid	seeQTL
rs1011266	KIFAP3	cis	parietal	SCAN
rs1011266	METTL18	cis	Artery Tibial	GTEx
rs1011266	METTL18	cis	Nerve Tibial	GTEx
rs1011266	METTL18	cis	Adipose Subcutaneous	GTEx
rs1011266	METTL18	cis	Artery Aorta	GTEx
rs1011266	METTL18	cis	Esophagus Muscularis	GTEx
rs1011266	SFT2D2	cis	cerebellum	SCAN
rs1011266	C1orf156	cis	uninvolved skin	skin_eQTL
rs1011266	GOLT1A	trans	cerebellum	SCAN
rs1011266	POGK	cis	cerebellum	SCAN
rs1011266	METTL18	cis	Muscle Skeletal	GTEx
rs1011266	ILDR2	cis	cerebellum	SCAN
rs1011266	SELL	cis	cerebellum	SCAN
rs1011266	C1orf156	cis	cerebellum	SCAN
rs1011266	C1orf156	cis	parietal	SCAN
rs1011266	TIPRL	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169644000-169649000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr1:169644600-169651600	Enhancers	Primary B cells from cord blood	blood
3	chr1:169644800-169647200	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:169644800-169647400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:169645000-169647200	Enhancers	Primary T cells from cord blood	blood
6	chr1:169645000-169647200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169645000-169647400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:169645000-169651600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:169645000-169652200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:169645200-169649400	Enhancers	GM12878-XiMat	blood
11	chr1:169645600-169650200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:169646000-169648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:169646200-169650000	Weak transcription	NHDF-Ad	bronchial
14	chr1:169646400-169648800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:169646800-169647800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:169646800-169648200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:169646800-169648200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:169646800-169648400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:169646800-169648400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:169646800-169648400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:169646800-169651800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:169647000-169648000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:169647000-169648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:169647000-169648200	Weak transcription	Dnd41	blood

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