Variant report

Variant	rs1883228
Chromosome Location	chr1:169677000-169677001
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	chr1:169674141..169677050-chr1:169763005..169764633,2	MCF-7	breast:
2	chr1:169669179..169671320-chr1:169675894..169677671,2	K562	blood:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1051091	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800469	0.83[EUR][1000 genomes]
rs10919227	0.80[EUR][1000 genomes]
rs12072966	0.90[CHB][hapmap]
rs12076368	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12079552	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12087033	0.90[CHB][hapmap]
rs12131780	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883229	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1961877	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2205847	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2205849	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2229569	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2298899	0.90[CHB][hapmap]
rs2420503	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2420505	0.83[CEU][hapmap]
rs35289447	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3766129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3917406	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3917413	0.86[EUR][1000 genomes]
rs3917428	0.90[CHB][hapmap]
rs3917430	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs3917432	0.90[CHB][hapmap]
rs3917435	0.91[ASN][1000 genomes]
rs3917436	0.94[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs3917444	0.87[EUR][1000 genomes]
rs3917449	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4265482	0.89[EUR][1000 genomes]
rs4427452	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4656189	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4656697	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs4656698	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4656701	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656703	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4656704	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4786	0.94[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs4987266	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4987270	0.87[EUR][1000 genomes]
rs4987285	0.94[CEU][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4987298	0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4987301	0.90[CHB][hapmap]
rs4987306	0.90[CHB][hapmap]
rs4987314	0.90[CHB][hapmap]
rs4987318	0.94[CEU][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4987320	0.90[CHB][hapmap]
rs4987322	0.90[CHB][hapmap]
rs4987328	0.90[CHB][hapmap]
rs5353	0.94[CEU][hapmap];0.95[TSI][hapmap]
rs5356	0.80[CHB][hapmap]
rs5359	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs58662634	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs59807249	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6427212	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs727909	0.87[EUR][1000 genomes]
rs7418242	0.90[CHB][hapmap]
rs7513119	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs932307	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs964555	0.90[CHB][hapmap]
rs964556	0.90[CHB][hapmap]
rs964557	0.90[CHB][hapmap]

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	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
3	nsv1009313	chr1:169661299-169680173	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv872541	chr1:169672360-169695815	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1883228	METTL18	cis	lung	GTEx
rs1883228	METTL18	cis	Adipose Subcutaneous	GTEx
rs1883228	METTL18	cis	Artery Tibial	GTEx
rs1883228	METTL18	cis	Thyroid	GTEx
rs1883228	METTL18	cis	Esophagus Mucosa	GTEx
rs1883228	SELL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169668000-169677400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
2	chr1:169670600-169678000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
3	chr1:169671200-169679400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr1:169672600-169677400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
5	chr1:169672600-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:169673200-169678400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
7	chr1:169674400-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
8	chr1:169675400-169677400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
9	chr1:169675400-169677400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:169675600-169678200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:169675800-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:169676000-169677000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:169676000-169677200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr1:169676000-169677200	Enhancers	Thymus	Thymus
15	chr1:169676000-169677800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:169676000-169679400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
17	chr1:169676200-169677200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:169676200-169678000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:169676400-169680600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr1:169676600-169677200	Active TSS	Primary T cells fromperipheralblood	blood
21	chr1:169676600-169677200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:169676600-169677200	Weak transcription	Fetal Thymus	thymus
23	chr1:169676600-169681400	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr1:169676800-169677000	Flanking Active TSS	GM12878-XiMat	blood
25	chr1:169676800-169677200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:169676800-169677200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr1:169676800-169677200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:169676800-169677400	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:169677000-169677200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:169677000-169677200	Active TSS	GM12878-XiMat	blood

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